R/gapit_functions.R
In mtmcgowan/FarmCPU: FarmCPU iteratively used fixed and random effect models for powerful and efficient genome-wide association studies (GWAS)
Defines functions
`GAPIT.0000`
GAPIT.AUC
`GAPIT.BIPH`
`GAPIT.Block`
`GAPIT.Bread`
`GAPIT.Burger`
`GAPIT.Bus`
`GAPIT.CVMergePC`
circle.plot
Densitplot
GAPIT.Circle.Manhatton.Plot
`GAPIT.Compress`
`GAPIT.Compression.Visualization`
`GAPIT.Create.Indicator`
`GAPIT.DP`
`GAPIT.EMMAxP3D`
`GAPIT.FDR.TypeI`
`GAPIT.Fragment`
`GAPIT.GS`
`GAPIT.GS.Visualization`
`GAPIT.Genotype`
`GAPIT.Genotype.View`
`GAPIT.HMP2Num`
`GAPIT.HapMap`
`GAPIT.IC`
`GAPIT.ID`
`GAPIT.Imputation`
`GAPIT.Interactive.GS`
`GAPIT.Interactive.Manhattan`
`GAPIT.Judge`
`GAPIT.Liner`
`GAPIT.Log`
`GAPIT.MAF`
`GAPIT.Main`
`GAPIT.Manhattan`
`GAPIT.Memory.Object`
`GAPIT.Memory`
`GAPIT.Multiple.Manhattan`
`GAPIT.Numericalization`
`GAPIT.PCA`
`GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure`
`GAPIT.Phenotype.PCA.View`
`GAPIT.Phenotype.Simulation`
`GAPIT.Phenotype.View`
`GAPIT.Power`
`GAPIT.Power.compare`
`GAPIT.Power.compare.plink`
`GAPIT.Prediction`
`GAPIT.Pruning`
`GAPIT.QC`
`GAPIT.QQ`
`GAPIT`
`GAPIT.ROC`
`GAPIT.RandomModel`
`GAPIT.RemoveDuplicate`
`GAPIT.Report`
`GAPIT.SS`
`GAPIT.SUPER.FastMLM`
`GAPIT.SUPER.GS`
`GAPIT.Specify`
`GAPIT.Table`
`GAPIT.Timmer`
`GAPIT.ZmatrixCompress`
`GAPIT.ZmatrixFormation`
`GAPIT.cross_validation.compare`
emma.kinship
emma.eigen.L
emma.eigen.L.wo.Z
emma.eigen.L.w.Z
emma.eigen.R
emma.eigen.R.wo.Z
emma.eigen.R.w.Z
emma.delta.ML.LL.wo.Z
emma.delta.ML.LL.w.Z
emma.delta.ML.dLL.wo.Z
emma.delta.ML.dLL.w.Z
emma.delta.REML.LL.wo.Z
emma.delta.REML.LL.w.Z
emma.delta.REML.dLL.wo.Z
emma.delta.REML.dLL.w.Z
emma.MLE
emma.REMLE
emma.ML.LRT
emma.REML.t
`GAPIT.emma.REMLE`
`GAPIT.kinship.VanRaden`
`GAPIT.kinship.ZHANG`
`GAPIT.kinship.loiselle`
`GAPIT.kinship.separation`
mlmm
mlmm_cof
`GAPIT.replaceNaN`
`GAPIT2`
`GAPIT.0000` <-
function(){
##############################################################################################
#GAPIT: Genome Association and Prediction Integrated Tool
#Objective 1: State of art methods for high power, accuracy and speed;
#Objective 2: User friendly by design, help documents, and web forum;
#Objective 3: Comprehensive output to interpret data and results;
#Objective 4: Informative tables and high quality figures for reports and publication;
#Methods implimented:
# 1. GLM (Structure or Q method for GWAS, Pritchard et. al. Genetics, 2000)
# 2. MLM (Q+K, Yu et. al. Nature Genetics, 2006)
# 3. gBLUP (Marker based kinship, Zhang et. al. Journal of Animal Science, 2007)
# 4. PCA (Zhao et. al. Plos Genetics, 2007)
# 5. EMMA (Kang et. al. Genetics, 2008)
# 6. CMLM (Zhang et. al. Nature Genetics, 2010)
# 7. EMMAx (Kang et. al. Nature Genetics, 2010)
# 8. P3D (Zhang et. al. Nature Genetics, 2010)
# 9. FaST-LMM (Lippert et. al. Nature Methods, 2011)
# 10. ECMLM (Li et. al. BMC Bioogy, 2014)
# 11. SUPER (Wang et. al. PLoS One, 2014)
#Designed by Zhiwu Zhang
#Authors of paper on Bioinformatics (2012, 28:2397-2399): Alex Lipka, Feng Tian, Qishan Wang, Xiaolei Liu, Meng Li,You Tang and Zhiwu Zhang
#Authors of paper on Plant Genome (2016, Vol 9, No. 2): You Tang, Xiaolei Liu, Jiabo Wang, Meng Li, Qishan Wang, Feng Tian, Zhongbin Su, Yuchun Pan, Di Liu, Alexander E. Lipka, Edward S. Buckler, and Zhiwu Zhang
if(!require(multtest))
{
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("multtest")
#source("http://www.bioconductor.org/biocLite.R")
#biocLite("multtest")
}
if(!require(gplots)) install.packages("gplots")
if(!require(LDheatmap)) install.packages("LDheatmap")
if(!require(genetics)) install.packages("genetics")
if(!require(ape)) install.packages("ape")
if(!require(EMMREML)) install.packages("EMMREML")
if(!require(scatterplot3d)) install.packages("scatterplot3d")
#if(!require(scatterplot3d)) install.packages("scatterplot3d")
# required_pkg = c("MASS", "data.table","biganalytics","ape", "magrittr","bigmemory", "gplots", "compiler", "scatterplot3d", "R.utils", "rrBLUP", "BGLR")
# missing_pkg = required_pkg[!(required_pkg %in% installed.packages()[,"Package"])]
# if(length(missing_pkg)) install.packages(missing_pkg, repos="http://cran.rstudio.com/")
if(!'multtest'%in% installed.packages()[,"Package"]){
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("snpStats")
#source("http://www.bioconductor.org/biocLite.R")
#biocLite("multtest")
#biocLite("snpStats")
}
GAPIT.Version="2018.08.18, GAPIT 3.0"
print(paste("All packages are loaded already ! ","GAPIT.Version is ",GAPIT.Version,sep=""))
return(GAPIT.Version)
}
#=============================================================================================
#Object: To calculate Area Under (ROC) Curve (AUC)
#Straitegy: NA
#Output: P value
#intput: beta-power and alpha-fdr or type I error
#Authors: Zhiwu Zhang
#Last update: December 18, 2015
##############################################################################################
GAPIT.AUC=function(beta=NULL,alpha=NULL){
n=length(beta)
#plot(alpha,beta,type="b")
db=beta[-1]-beta[-n]
da=1-.5*(alpha[-1]+alpha[-n])
ab=da*db
AUC=sum(ab)
return(AUC)
}
#=============================================================================================
#Object: To generate binary phenotype
#Straitegy: NA
#Output: binary phenotype (0 and 1's)
#intput: genetic effect (x), hertiability (h2) and ratio of 1's (r)
#Authors: Zhiwu Zhang
#Last update: March 18, 2016
##############################################################################################
`GAPIT.BIPH` <-
function(x=0,h2=.5,r=.25){
#To assign probability for given standard normal variable x and h2
#Author: Zhiwu Zhang
#Last update: Febuary 27, 2016
p=pnorm(x)
srp=1-p-r
sh=1/(1-sqrt(h2))
adj=(r-.5)*(1-sqrt(h2))
f=1/(1+exp(sh*srp))+adj
return(f)
}
#=============================================================================================
`GAPIT.Block` <-
function(Z,GA,KG){
#Object: To split a group kinship into two blocks containing individuals with and without phenotype
#Output: GAU,KW,KO,KWO
#Authors: Zhiwu Zhang and Alex Lipka
# Last update: April 14, 2011
##############################################################################################
# To separate group kiship into two blocks: with and without phenotype.
# A group goes to with phenotype as loog as it has one phenotyped individual.
#find position in group assignment (GA) for the individual associate with phenotype (specified by Z)
#taxa=unique(intersect(as.matrix(Z[1,-1]),GA[,1]))
taxa.Z=as.matrix(Z[1,-1])
taxa.GA=as.matrix(GA[,1])
position=taxa.GA%in%taxa.Z
#Initial block as 2
GAU=cbind(GA,2)
#Assign block as 1 if the individual has phenotype
GAU[position,3]=1
#Modify the non-phenotyped individuals if they in a group with phenotyped individuals
#To find the groups with phenotyped individuals
#update block assignment for all these groups
#get list of group that should be block 1
#grp.12=as.matrix(unique(GAU[,2]))
#grp.1=as.matrix(unique(GAU[which(GAU[,3]==1),2]))
#grp.2= as.matrix(setdiff(grp.12,grp.1))
grp.12=as.matrix(as.vector(unique(GAU[,2])) ) #unique group
grp.1=as.matrix(as.vector(unique(GAU[which(GAU[,3]==1),2])) ) #unique phenotyped group
grp.2= as.matrix(as.vector(setdiff(grp.12,grp.1))) #unique unphenotyped group
numWithout=length(grp.2)
order.1=1:length(grp.1)
order.2=1:length(grp.2)
if(numWithout >0) grpblock=as.matrix(rbind(cbind(grp.1,1,order.1), cbind(grp.2, 2, order.2)))
if(numWithout==0) grpblock=as.matrix( cbind(grp.1,1,order.1), )
order.block=order(as.matrix(GAU[,3]))
colnames(grpblock)=c("grp","block","ID")
#Indicators: 1-Phenotype, 1.5- unphenotyped but in a group with other phenotyped, 2-rest (Zhiwu, Dec 7,2012)
#GAU0 <- merge(GAU[order.block,-3], grpblock, by.x = "X2", by.y = "grp")
#GAU=GAU0[,c(2,1,3,4)]
#print(head(GAU))
GAU1 <- merge(GAU[order.block,], grpblock, by.x = "X2", by.y = "grp")
#print(GAU1)
GAU1[,4]=(as.numeric(GAU1[,3])+as.numeric(GAU1[,4]))/2
#print(GAU1)
GAU=GAU1[,c(2,1,4,5)]
KW=KG[grp.1,grp.1]
KO=KG[grp.2,grp.2]
KWO=KG[grp.1,grp.2]
#write.table(GAU, "GAU.txt", quote = FALSE, sep = "\t", row.names = TRUE,col.names = TRUE)
#print("GAPIT.Block accomplished successfully!")
return(list(GAU=GAU,KW=KW,KO=KO,KWO=KWO))
}#The function GAPIT.Block ends here
#=============================================================================================
`GAPIT.Bread` <-
function(Y=NULL,CV=NULL,Z=NULL,KI=NULL,GK=NULL,GD=NULL,GM=NULL,
method=NULL,delta=NULL,vg=NULL,ve=NULL,LD=0.01,GTindex=NULL,
file.output=TRUE,opt="extBIC"){
#Object: To calculate p-values of SNPs by using method of GLM, MLM, CMLM, FaST, SUPER and DC
#Straitegy: NA
#Output: GWAS, GPS,REMLs,vg,ve,delta
#intput:
#Y: phenotype with columns of taxa,Y1,Y2...
#CV: covariate variables with columns of taxa, v1,v2...
#GD: same as GK. This is the genotype to screen, the columns are taxa,SNP1,SNP2,...
#GK: Genotype data in numerical format, taxa goes to row and snp go ti columns. the first column is taxa
#GM: Genotype map with columns of snpID,chromosome and position
#method: Options are GLM, MLM, CMLM, FaST, SUPER ,FARM-CPU and DC
#Authors: Zhiwu Zhang
#Last update: November 2, 2011
##############################################################################################
#print("GAPIT.SUPER in progress...")
#Performing first screening with GLM
if(method=="GLM"){
#print("---------------screening by GLM----------------------------------")
#print(GTindex)
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
model=("GLM"),
QC=FALSE,
GTindex=GTindex,
file.output=file.output
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with MLM
if(method=="MLM"){
#print("---------------screening by MLM----------------------------------")
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
group.from=nrow(Y),
group.to=nrow(Y),
QC=FALSE,
GTindex=GTindex,
file.output=file.output
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with Compressed MLM
if(method=="CMLM"){
#print("---------------screening by CMLM----------------------------------")
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
group.from=1,
group.to=nrow(Y),
QC=FALSE,
GTindex=GTindex,
file.output=file.output
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with FaST-LMM
if(method=="FaST" | method=="SUPER"| method=="DC")
{
GWAS=NULL
GPS=NULL
if(!is.null(vg) & !is.null(vg) & is.null(delta)) delta=ve/vg
if(is.null(vg) & is.null(ve))
{
myFaSTREML=GAPIT.get.LL(pheno=matrix(Y[,-1],nrow(Y),1),geno=NULL,snp.pool=as.matrix(GK[,-1]),X0=as.matrix(cbind(matrix(1,nrow(CV),1),CV[,-1])))
#print("Transfer data...")
REMLs=-2*myFaSTREML$LL
delta=myFaSTREML$delta
vg=myFaSTREML$vg
ve=myFaSTREML$ve
#GPS=myFaSTREML$GPS
}
mySUPERFaST=GAPIT.SUPER.FastMLM(ys=matrix(Y[,-1],nrow(Y),1),X0=as.matrix(cbind(matrix(1,nrow(CV),1),CV[,-1])),snp.pool=as.matrix(GK[-1]), xs=as.matrix(GD[GTindex,-1]),vg=vg,delta=delta,LD=LD,method=method)
GWAS=cbind(GM,mySUPERFaST$ps,mySUPERFaST$stats,mySUPERFaST$dfs,mySUPERFaST$effect)
}#End of if(method=="FaST" | method=="SUPER")
#FarmCPU
if(method=="FarmCPU")
{
if(!require(bigmemory)) install.packages("bigmemory")
if(!require(biganalytics)) install.packages("biganalytics")
library(bigmemory) #for FARM-CPU
library(biganalytics) #for FARM-CPU
if(!exists('FarmCPU', mode='function'))source("http://www.zzlab.net/FarmCPU/FarmCPU_functions.txt")#web source code
colnames(GM)[1]="SNP"
myFarmCPU=FarmCPU(
Y=Y,#Phenotype
GD=GD,#Genotype
GM=GM,#Map information
CV=CV[,2:ncol(CV)],
file.output=T
)
xs=t(GD[,-1])
#print(dim(xs))
gene_taxa=colnames(GD)[-1]
ss=apply(xs,1,sum)
ns=nrow(GD)
storage=cbind(.5*ss/ns,1-.5*ss/ns)
maf=as.data.frame(cbind(gene_taxa,apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)))
colnames(maf)=c("SNP","maf")
nobs=ns
#print(dim(myFarmCPU$GWAS))
#print(length(maf))
myFarmCPU$GWAS=merge(myFarmCPU$GWAS[,-5],maf, by.x = "SNP", by.y = "SNP")
GWAS=cbind(myFarmCPU$GWAS,nobs)
GWAS=GWAS[order(GWAS$P.value),]
#colnames(GWAS)=c("SNP","Chromosome","Position","mp","mc","maf","nobs")
GPS=myFarmCPU$Pred
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
#colnames(GPS)[3]=c("Prediction")
}
#MLMM
if(method=="MLMM")
{
print(" GWAS by MLMM method !!")
Y=Y[!is.na(Y[,2]),]
taxa_Y=as.character(Y[,1])
taxa_GD=as.character(GD[,1])
taxa_CV=as.character(CV[,1])
GD=GD[taxa_GD%in%taxa_Y,]
CV=CV[taxa_CV%in%taxa_Y,]
#print(dim(Y))
#print(dim(GD))
#print(dim(CV))
KI= GAPIT.kinship.VanRaden(snps=as.matrix(GD[,-1]))
colnames(KI)=as.character(GD[,1])
if(is.null(CV))
{
mymlmm=mlmm(
Y=Y[,2],#Phenotype
X=as.matrix(GD[,-1]),#Genotype
K=as.matrix(KI),
#cofs=CV[,2:ncol(CV)],
nbchunks = 2, maxsteps = 10, thresh = 1.2 * 10^-5)
}else{
mymlmm=mlmm_cof(
Y=Y[,2],#Phenotype
X=as.matrix(GD[,-1]),#Genotype
K=as.matrix(KI),
cofs=as.matrix(CV[,2:ncol(CV)]),
nbchunks = 2, maxsteps = 10, thresh = 1.2 * 10^-5)
}
if(opt=='extBIC'){
GWAS_result=mymlmm$opt_extBIC$out
}
if(opt=='mbonf'){
GWAS_result=mymlmm$opt_mbonf$out
}
if(opt=='thresh'){
GWAS_result=mymlmm$opt_thresh$out
}
colnames(GWAS_result)=c("SNP","P.value")
xs=t(GD[,-1])
#print(dim(xs))
gene_taxa=colnames(GD)[-1]
colnames(GM)=c("SNP","Chromosome","position")
ss=apply(xs,1,sum)
ns=nrow(GD)
storage=cbind(.5*ss/ns,1-.5*ss/ns)
maf=as.data.frame(cbind(gene_taxa,apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)))
colnames(maf)=c("SNP","maf")
nobs=ns
GWAS_GM=merge(GM,GWAS_result, by.x = "SNP", by.y = "SNP")
mc=matrix(NA,nrow(GWAS_GM),1)
GWAS_GM=cbind(GWAS_GM,mc)
GWAS_GM_maf=merge(GWAS_GM,maf, by.x = "SNP", by.y = "SNP")
GWAS=cbind(GWAS_GM_maf,nobs)
#print(head(GWAS))
GWAS=GWAS[order(GWAS$P.value),]
GPS=NULL
#h2=mymlmm$step_table$h2[length(mymlmm$step_table$h2)]
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
colnames(GWAS)=c("SNP","Chromosome","Position","P.value","effec","maf","nobs")
}
#print("GAPIT.Bread succeed!")
return (list(GWAS=GWAS, GPS=GPS,REMLs=REMLs,vg=vg,ve=ve,delta=delta))
} #end of GAPIT.Bread
#=============================================================================================
`GAPIT.Burger` <-
function(Y=NULL,CV=NULL,GK=NULL){
#Object: To calculate likelihood, variances and ratio
#Straitegy: NA
#Output: P value
#intput:
#Y: phenotype with columns of taxa,Y1,Y2...
#CV: covariate variables with columns of taxa,v1,v2...
#GK: Genotype data in numerical format, taxa goes to row and snp go to columns. the first column is taxa (same as GAPIT.bread)
#Authors: Xiaolei Liu ,Jiabo Wang and Zhiwu Zhang
#Last update: November 2, 2015
##############################################################################################
#print("GAPIT.Burger in progress...")
if(!is.null(CV)){
#CV=as.matrix(CV)#change CV to a matrix when it is a vector xiaolei changed here
#theCV=as.matrix(cbind(matrix(1,nrow(CV),1),CV)) ###########for FarmCPU
theCV=as.matrix(cbind(matrix(1,nrow(CV),1),CV[,-1])) #reseted by Jiabo ,CV frame is wrong,and not rm taxa
#############for GAPIT other method GWAS
}else{
theCV=matrix(1,nrow(Y),1)
}
#handler of single column GK
n=nrow(GK)
m=ncol(GK)
if(m>2){
theGK=as.matrix(GK[,-1])
}else{
theGK=matrix(GK[,-1],n,1)
}
myFaSTREML=GAPIT.get.LL(pheno=matrix(Y[,-1],nrow(Y),1),geno=NULL,snp.pool=theGK,X0=theCV )
REMLs=-2*myFaSTREML$LL
delta=myFaSTREML$delta
vg=myFaSTREML$vg
ve=myFaSTREML$ve
#print("GAPIT.Burger succeed!")
return (list(REMLs=REMLs,vg=vg,ve=ve,delta=delta))
} #end of GAPIT.Burger.Bus
#=============================================================================================
`GAPIT.Bus`<-
function(Y=NULL,CV=NULL,Z=NULL,GT=NULL,KI=NULL,GK=NULL,GD=NULL,GM=NULL,
WS=c(1e0,1e3,1e4,1e5,1e6,1e7),alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),
method=NULL,delta=NULL,vg=NULL,ve=NULL,LD=0.01,GTindex=NULL,
cutOff=0.01,Multi_iter=FASLE,windowsize=5e10,
p.threshold=NA,QTN.threshold=0.01,maf.threshold=0.03,
method.GLM="FarmCPU.LM",method.sub="reward",method.sub.final="reward",method.bin="static",
DPP=1000000,bin.size=c(5e5,5e6,5e7),bin.selection=seq(10,100,10),
file.output=TRUE,opt="extBIC"){
#Object: To license data by method
#Output: Coresponding numerical value
# This function is used to run multiple method, Thanks MLMM FarmCPU Blink to share program and code.
#Authors: Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
GR=NULL
#print(head(CV))
if(method=="GLM"){
#print("---------------screening by GLM----------------------------------")
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
group.from=0,
group.to=0,
QC=FALSE,
GTindex=GTindex,
file.output=F
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with MLM
if(method=="MLM"){
#print("---------------screening by MLM----------------------------------")
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
group.from=nrow(Y),
group.to=nrow(Y),
QC=FALSE,
GTindex=GTindex,
file.output=F
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with Compressed MLM
if(method=="CMLM"){
#print("---------------screening by CMLM----------------------------------")
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
group.from=1,
group.to=nrow(Y),
QC=FALSE,
GTindex=GTindex,
file.output=F
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with FaST-LMM
if(method=="FaST" | method=="SUPER"| method=="DC")
{
GWAS=NULL
GPS=NULL
if(!is.null(vg) & !is.null(vg) & is.null(delta)) delta=ve/vg
if(is.null(vg) & is.null(ve))
{
#print("!!!!!!!!!!!!!!!!")
myFaSTREML=GAPIT.get.LL(pheno=matrix(Y[,-1],nrow(Y),1),geno=NULL,snp.pool=as.matrix(GK[,-1]),X0=as.matrix(cbind(matrix(1,nrow(CV),1),CV[,-1])))
#print(myFaSTREML)
#print("Transfer data...")
REMLs=-2*myFaSTREML$LL
delta=myFaSTREML$delta
vg=myFaSTREML$vg
ve=myFaSTREML$ve
#GPS=myFaSTREML$GPS
}
mySUPERFaST=GAPIT.SUPER.FastMLM(ys=matrix(Y[,-1],nrow(Y),1),X0=as.matrix(cbind(matrix(1,nrow(CV),1),CV[,-1])),snp.pool=as.matrix(GK[-1]), xs=as.matrix(GD[GTindex,-1]),vg=vg,delta=delta,LD=LD,method=method)
GWAS=cbind(GM,mySUPERFaST$ps,mySUPERFaST$stats,mySUPERFaST$dfs,mySUPERFaST$effect)
}#End of if(method=="FaST" | method=="SUPER")
if(method=="FarmCPU")
{
if(!require(bigmemory)) install.packages("bigmemory")
if(!require(biganalytics)) install.packages("biganalytics")
library(bigmemory) #for FARM-CPU
library(biganalytics) #for FARM-CPU
if(!exists('FarmCPU', mode='function'))source("http://www.zzlab.net/FarmCPU/FarmCPU_functions.txt")#web source code
colnames(GM)[1]="SNP"
#print(GTindex)
if(!is.null(CV))
{ farmcpuCV=CV[,2:ncol(CV)]
}else{
farmcpuCV=NULL
}
#print(head(farmcpuCV))
# print(dim(GD))
# print(dim(farmcpuCV))
# print(dim(Y))
myFarmCPU=FarmCPU(
Y=Y,#Phenotype
GD=GD,#Genotype
GM=GM,#Map information
CV=farmcpuCV,
cutOff=cutOff,p.threshold=p.threshold,QTN.threshold=QTN.threshold,
maf.threshold=maf.threshold,method.GLM=method.GLM,method.sub=method.sub,
method.sub.final=method.sub.final,method.bin=method.bin,bin.size=c(5e5,5e6,5e7),bin.selection=seq(10,100,10),
file.output=T
)
GWAS=myFarmCPU$GWAS
xs=t(GD[,-1])
# gene_taxa=colnames(GD)[-1]
ss=apply(xs,1,sum)
ns=nrow(GD)
# storage=cbind(.5*ss/ns,1-.5*ss/ns)
# #maf=as.data.frame(cbind(gene_taxa,apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)))
# colnames(maf)=c("SNP","maf")
nobs=ns
# #GWAS=merge(GWAS[,-5],maf, by.x = "SNP", by.y = "SNP")
# GWAS=merge(GWAS[,-5],maf, by.x = "SNP", by.y = "SNP") #Jiabo modified at 2019.3.25
GWAS=cbind(GWAS,nobs)
maf=apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)
GWAS$maf=maf
#print(head(GWAS))
#print("!!!!!!!!!!!!!")
#print(Multi_iter)
if(Multi_iter)
{
sig=GWAS[GWAS[,4]<(cutOff/(nrow(GWAS))),1:5]
sig=sig[!is.na(sig[,4]),]
#windowsize=500000000
sig_position=as.numeric(as.matrix(sig[,1:3])[,2])*10^10+as.numeric(as.matrix(sig[,1:3])[,3])
sig=sig[order(sig_position),]
sig_position=sig_position[order(sig_position)]
sig_diff=abs(sig_position-c(sig_position[-1],0))
sig_diff_index=sig_diff<windowsize
GWAS0=GWAS
#####################
n=nrow(sig)
print("The number of significant markers is")
print(n)
if(n>0)
{
for(i in 1:n)
{
aim_marker=sig[i,]
#print(aim_marker)
aim_order=as.numeric(rownames(aim_marker))
aim_chro=as.character(aim_marker[,2])
aim_position=as.numeric(as.character(aim_marker[,3]))
position=as.numeric(as.matrix(GM)[,3])
aim_area=GM[,2]==aim_chro&position<(aim_position+windowsize)&position>(aim_position-windowsize)
aim_matrix=as.matrix(table(aim_area))
#print(aim_area)
#print(setequal(aim_area,logical(0)))
if(setequal(aim_area,logical(0))) next
if(aim_matrix[rownames(aim_matrix)=="TRUE",1]<10) next
aim_area[GM[,1]==aim_marker[,1]]=FALSE
secondGD=GD[,c(TRUE,aim_area)]
secondGM=GM[aim_area,]
myGAPIT_Second <- FarmCPU(
Y=Y,
GD=secondGD,
GM=secondGM,
CV=farmcpuCV,
file.output=T
)
Second_GWAS= myGAPIT_Second$GWAS [,1:4]
Second_GWAS[is.na(Second_GWAS[,4]),4]=1
orignal_GWAS=GWAS[aim_area,]
GWAS_index=match(Second_GWAS[,1],GWAS[,1])
#test_GWAS=GWAS
GWAS[GWAS_index,4]=Second_GWAS[,4]
}
}
}
#GWAS=GWAS[order(GWAS$P.value),]
#colnames(GWAS)=c("SNP","Chromosome","Position","mp","mc","maf","nobs")
#print(head(GWAS))
GWAS[,2]=as.numeric(as.character(GWAS[,2]))
GWAS[,3]=as.numeric(as.character(GWAS[,3]))
#rint(head(GWAS))
nobs=ns
# #GWAS=merge(GWAS[,-5],maf, by.x = "SNP", by.y = "SNP")
# GWAS=merge(GWAS[,-5],maf, by.x = "SNP", by.y = "SNP") #Jiabo modified at 2019.3.25
#GWAS=cbind(GWAS,nobs)
#print(head(GWAS))
GWAS=GWAS[,c(1:5,7,6)]
GR=GAPIT.RandomModel(Y=Y,X=GD[,-1],GWAS=GWAS,CV=cbind(Y[,1],farmcpuCV),cutOff=cutOff,GT=GT)
GPS=myFarmCPU$Pred
#colnames(GPS)[3]=c("Prediction")
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
#print(dim(GWAS))
#print(head(GWAS))
print("FarmCPU has been done succeedly!!")
}
if(method=="BlinkC")
{
blink_GD=t(GD[,-1])
blink_GM=GM
blink_Y=Y
blink_Y[is.na(blink_Y)]="NaN"
colnames(blink_Y)=c("taxa","trait1")
blink_CV=CV
write.table(blink_GD,"myData.dat",quote=F,col.names=F,row.names=F)
write.table(blink_GM,"myData.map",quote=F,col.names=T,row.names=F)
write.table(blink_Y,"myData.txt",quote=F,col.names=T,row.names=F)
if(!is.null(CV))
{
write.table(blink_CV,"myData.cov",quote=F,col.names=T,row.names=F)
}else{
system("rm myData.cov")
}
system("./blink --gwas --file myData --numeric")
result=read.table("trait1_GWAS_result.txt",head=T)
result=result[,c(1,2,3,5,4)]
xs=t(GD[,-1])
#print(dim(xs))
gene_taxa=colnames(GD)[-1]
ss=apply(xs,1,sum)
ns=nrow(GD)
storage=cbind(.5*ss/ns,1-.5*ss/ns)
maf=result[,5]
#colnames(maf)=c("SNP","maf")
nobs=ns
effect=rep(NA,length(nobs))
#myFarmCPU$GWAS=merge(myFarmCPU$GWAS[,-5],maf, by.x = "SNP", by.y = "SNP")
GWAS=cbind(result[,1:4],effect)
GWAS=cbind(GWAS,maf)
GWAS=cbind(GWAS,nobs)
GWAS[,2]=as.numeric(as.character(GWAS[,2]))
GWAS[,3]=as.numeric(as.character(GWAS[,3]))
#print(dim(GWAS))
#GWAS=GWAS[order(GWAS$P.value),]
colnames(GWAS)=c("SNP","Chromosome","Position","P.value","effec","maf","nobs")
GPS=NULL
#colnames(GPS)[3]=c("Prediction")
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
}
if(method=="Blink")
{
if(!require(devtools)) install.packages("devtools")
if(!require(BLINK)) devtools::install_github("YaoZhou89/BLINK")
#source("http://zzlab.net/GAPIT/gapit_functions.txt")
source("http://zzlab.net/FarmCPU/FarmCPU_functions.txt")
blink_GD=t(GD[,-1])
blink_GM=GM
blink_Y=Y
blink_CV=NULL
if(!is.null(CV))blink_CV=CV[,-1]
#print(head(blink_CV))
library(BLINK)
myBlink=Blink(Y=blink_Y,GD=blink_GD,GM=blink_GM,CV=blink_CV,maxLoop=10,time.cal=T)
#print(head(myBlink$GWAS))
GWAS=myBlink$GWAS[,1:4]
#print(str(myBlink))
ns=nrow(GD)
nobs=ns
effect=rep(NA,length(nobs))
xs=t(GD[,-1])
ss=apply(xs,1,sum)
#storage=cbind(.5*ss/ns,1-.5*ss/ns)
maf=apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)
GWAS=cbind(GWAS,maf)#, by.x = "SNP", by.y = "SNP") #Jiabo modified at 2019.3.25
GWAS=cbind(GWAS,effect)
GWAS=cbind(GWAS,nobs)
# gene_taxa=as.character(blink_GM[,1])
# ss=apply(blink_GD,1,sum)
# ns=nrow(GD)
# nobs=ns
# storage=cbind(.5*ss/ns,1-.5*ss/ns)
# maf=as.data.frame(cbind(gene_taxa,apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)))
# colnames(maf)=c("SNP","maf")
# effect=rep(NA,length(nobs))
# GWAS=cbind(GWAS,effect)
# GWAS=cbind(GWAS,maf)
# GWAS=cbind(GWAS,nobs)
# GWAS[,2]=as.numeric(as.character(GWAS[,2]))
# GWAS[,3]=as.numeric(as.character(GWAS[,3]))
# GPS=myBlink$Pred
#colnames(GPS)[3]=c("Prediction")
if(Multi_iter)
{
sig=GWAS[GWAS[,4]<(cutOff/(nrow(GWAS))),1:5]
sig=sig[!is.na(sig[,4]),]
#windowsize=500000000
sig_position=as.numeric(as.matrix(sig[,1:3])[,2])*10^10+as.numeric(as.matrix(sig[,1:3])[,3])
sig=sig[order(sig_position),]
sig_position=sig_position[order(sig_position)]
sig_diff=abs(sig_position-c(sig_position[-1],0))
sig_diff_index=sig_diff<windowsize
GWAS0=GWAS
#####################
n=nrow(sig)
print("The number of significant markers is")
print(n)
if(n>0)
{
for(i in 1:n)
{
aim_marker=sig[i,]
#print(aim_marker)
aim_order=as.numeric(rownames(aim_marker))
aim_chro=as.character(aim_marker[,2])
aim_position=as.numeric(as.character(aim_marker[,3]))
position=as.numeric(as.matrix(GM)[,3])
aim_area=GM[,2]==aim_chro&position<(aim_position+windowsize)&position>(aim_position-windowsize)
aim_matrix=as.matrix(table(aim_area))
if(setequal(aim_area,logical(0))) next
if(aim_matrix[rownames(aim_matrix)=="TRUE",1]<10) next
aim_area[GM[,1]==aim_marker[,1]]=FALSE
secondGD=GD[,c(TRUE,aim_area)]
secondGM=GM[aim_area,]
myGAPIT_Second =Blink(Y=Y,GD=secondGD,GM=secondGM,CV=blink_CV,maxLoop=10,time.cal=T)
#print(head(myBlink$GWAS))
#GWAS=myBlink$GWAS[,1:4]
Second_GWAS= myGAPIT_Second$GWAS [,1:4]
Second_GWAS[is.na(Second_GWAS[,4]),4]=1
orignal_GWAS=GWAS[aim_area,]
GWAS_index=match(Second_GWAS[,1],GWAS[,1])
#test_GWAS=GWAS
GWAS[GWAS_index,4]=Second_GWAS[,4]
}
}
}
#GWAS=GWAS[order(GWAS$P.value),]
#colnames(GWAS)=c("SNP","Chromosome","Position","mp","mc","maf","nobs")
#print(head(GWAS))
GWAS[,2]=as.numeric(as.character(GWAS[,2]))
GWAS[,3]=as.numeric(as.character(GWAS[,3]))
#rint(head(GWAS))
GPS=myBlink$Pred
#colnames(GPS)[3]=c("Prediction")
#print(head(GWAS))
GWAS=GWAS[,c(1:5,7,6)]
GR=GAPIT.RandomModel(Y=blink_Y,X=GD[,-1],GWAS=GWAS,CV=CV,cutOff=cutOff,GT=GT)
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
#print(dim(GWAS))
#print(head(GWAS))
print("Bink R is done !!!!!")
}
if(method=="MLMM")
{
print("GWAS by MLMM method !!")
Y=Y[!is.na(Y[,2]),]
taxa_Y=as.character(Y[,1])
taxa_GD=as.character(GD[,1])
taxa_CV=as.character(CV[,1])
GD=GD[taxa_GD%in%taxa_Y,]
CV=CV[taxa_CV%in%taxa_Y,]
#print(dim(Y))
#print(dim(GD))
if(is.null(KI))
{
KI= GAPIT.kinship.VanRaden(snps=as.matrix(GD[,-1]))
colnames(KI)=as.character(GD[,1])
}else{
print("The Kinship is provided by user !!")
KI=KI[,-1]
#colnames(KI)=as.character(GD[,1])
taxa_KI=as.character(colnames(KI))
KI=KI[taxa_KI%in%as.character(GD[,1]),taxa_KI%in%as.character(GD[,1])]
}
if(ncol(KI)!=nrow(GD)) print("Please make sure dim of K equal number of GD !!")
# print(dim(KI))
# print(dim(GD))
# print(KI[1:5,1:5])
if(is.null(CV))
{
mymlmm=mlmm(
Y=Y[,2],#Phenotype
X=as.matrix(GD[,-1]),#Genotype
K=as.matrix(KI),
#cofs=CV[,2:ncol(CV)],
nbchunks = 2, maxsteps = 10, thresh = 1.2 * 10^-5)
}else{
mymlmm=mlmm_cof(
Y=Y[,2],#Phenotype
X=as.matrix(GD[,-1]),#Genotype
K=as.matrix(KI),
cofs=as.matrix(CV[,2:ncol(CV)]),
nbchunks = 2, maxsteps = 10, thresh = 1.2 * 10^-5)
}
if(opt=='extBIC'){
GWAS_result=mymlmm$opt_extBIC$out
}
if(opt=='mbonf'){
GWAS_result=mymlmm$opt_mbonf$out
}
if(opt=='thresh'){
GWAS_result=mymlmm$opt_thresh$out
}
colnames(GWAS_result)=c("SNP","P.value")
xs=t(GD[,-1])
#print(dim(xs))
gene_taxa=colnames(GD)[-1]
colnames(GM)=c("SNP","Chromosome","position")
ss=apply(xs,1,sum)
ns=nrow(GD)
storage=cbind(.5*ss/ns,1-.5*ss/ns)
maf=as.data.frame(cbind(gene_taxa,apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)))
colnames(maf)=c("SNP","maf")
nobs=ns
GWAS_GM=merge(GM,GWAS_result, by.x = "SNP", by.y = "SNP")
mc=matrix(NA,nrow(GWAS_GM),1)
GWAS_GM=cbind(GWAS_GM,mc)
#print(head(GWAS_GM))
#print(head(maf))
#maf=NULL
GWAS_GM_maf=merge(GWAS_GM,maf, by.x = "SNP", by.y = "SNP")
GWAS=cbind(GWAS_GM_maf,nobs)
#print(head(GWAS))
GWAS=GWAS[order(GWAS$P.value),]
GWAS[,2]=as.numeric(as.character(GWAS[,2]))
GWAS[,3]=as.numeric(as.character(GWAS[,3]))
GPS=NULL
#h2=mymlmm$step_table$h2[length(mymlmm$step_table$h2)]
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
colnames(GWAS)=c("SNP","Chromosome","Position","P.value","effect","maf","nobs")
}
#print("GAPIT.Bus succeed!")
return (list(GWAS=GWAS, GPS=GPS,REMLs=REMLs,vg=vg,ve=ve,delta=delta,GVs=GR$GVs))
} #end of GAPIT.Bus
#=============================================================================================
`GAPIT.CVMergePC` <-
function(X,Y){
#Object: To convert character SNP genotpe to numerical
#Output: Coresponding numerical value
#Authors: Feng Tian and Zhiwu Zhang
# Last update: May 30, 2011
##############################################################################################
#Z=X+Y
Z <- merge(X, Y, by.x = colnames(X)[1], by.y = colnames(Y)[1])
return(Z)
}#end of GAPIT.CVMergePCfunction
#=============================================================================================
########## These three functions come from MVP package, Jiabo did some modifications
########## Following Apache License, we thank MVP developper to build these functions.
########## 1 creat P value scale in addtitional chromsome
########## 2 set col is same as GAPIT
########## 3
circle.plot <- function(myr,type="l",x=NULL,lty=1,lwd=1,col="black",add=TRUE,n.point=1000)
{
curve(sqrt(myr^2-x^2),xlim=c(-myr,myr),n=n.point,ylim=c(-myr,myr),type=type,lty=lty,col=col,lwd=lwd,add=add)
curve(-sqrt(myr^2-x^2),xlim=c(-myr,myr),n=n.point,ylim=c(-myr,myr),type=type,lty=lty,col=col,lwd=lwd,add=TRUE)
}
Densitplot <- function(
map,
col=c("darkblue", "white", "red"),
main="SNP Density",
bin=1e6,
band=3,
width=5,
legend.len=10,
legend.max=NULL,
legend.pt.cex=3,
legend.cex=1,
legend.y.intersp=1,
legend.x.intersp=1,
plot=TRUE
)
{ #print(head(map))
map <- as.matrix(map)
map <- map[!is.na(map[, 2]), ]
map <- map[!is.na(map[, 3]), ]
map <- map[map[, 2] != 0, ]
#map <- map[map[, 3] != 0, ]
options(warn = -1)
max.chr <- max(as.numeric(map[, 2]), na.rm=TRUE)
if(is.infinite(max.chr)) max.chr <- 0
map.xy.index <- which(!as.numeric(map[, 2]) %in% c(0 : max.chr))
if(length(map.xy.index) != 0){
chr.xy <- unique(map[map.xy.index, 2])
for(i in 1:length(chr.xy)){
map[map[, 2] == chr.xy[i], 2] <- max.chr + i
}
}
map <- map[order(as.numeric(map[, 2]), as.numeric(map[, 3])), ]
chr <- as.numeric(map[, 2])
pos <- as.numeric(map[, 3])
chr.num <- unique(chr)
#print(chr.num)
chorm.maxlen <- max(pos)
if(plot) plot(NULL, xlim=c(0, chorm.maxlen + chorm.maxlen/10), ylim=c(0, length(chr.num) * band + band), main=main,axes=FALSE, xlab="", ylab="", xaxs="i", yaxs="i")
pos.x <- list()
col.index <- list()
maxbin.num <- NULL
#print(chr.num)
for(i in 1 : length(chr.num)){
pos.x[[i]] <- pos[which(chr == chr.num[i])]
cut.len <- ceiling((max(pos.x[[i]]) - min(pos.x[[i]])) / bin)
if(cut.len <= 1){
col.index[[i]] = 1
}else{
cut.r <- cut(pos.x[[i]], cut.len, labels=FALSE)
eachbin.num <- table(cut.r)
#print(eachbin.num)
maxbin.num <- c(maxbin.num, max(eachbin.num))
col.index[[i]] <- rep(eachbin.num, eachbin.num)
}
}
Maxbin.num <- max(maxbin.num)
maxbin.num <- Maxbin.num
if(!is.null(legend.max)){
maxbin.num <- legend.max
}
#print(col)
#print(maxbin.num)
col=colorRampPalette(col)(maxbin.num)
col.seg=NULL
for(i in 1 : length(chr.num)){
if(plot) polygon(c(0, 0, max(pos.x[[i]]), max(pos.x[[i]])),
c(-width/5 - band * (i - length(chr.num) - 1), width/5 - band * (i - length(chr.num) - 1),
width/5 - band * (i - length(chr.num) - 1), -width/5 - band * (i - length(chr.num) - 1)), col="grey", border="grey")
if(!is.null(legend.max)){
if(legend.max < Maxbin.num){
col.index[[i]][col.index[[i]] > legend.max] <- legend.max
}
}
col.seg <- c(col.seg, col[round(col.index[[i]] * length(col) / maxbin.num)])
if(plot) segments(pos.x[[i]], -width/5 - band * (i - length(chr.num) - 1), pos.x[[i]], width/5 - band * (i - length(chr.num) - 1),
col=col[round(col.index[[i]] * length(col) / maxbin.num)], lwd=1)
}
if(length(map.xy.index) != 0){
for(i in 1:length(chr.xy)){
chr.num[chr.num == max.chr + i] <- chr.xy[i]
}
}
chr.num <- rev(chr.num)
if(plot) mtext(at=seq(band, length(chr.num) * band, band),text=paste("Chr", chr.num, sep=""), side=2, las=2, font=1, cex=0.6, line=0.2)
if(plot) axis(3, at=seq(0, chorm.maxlen, length=10), labels=c(NA, paste(round((seq(0, chorm.maxlen, length=10))[-1] / 1e6, 0), "Mb", sep="")),
font=1, cex.axis=0.8, tck=0.01, lwd=2, padj=1.2)
# image(c(chorm.maxlen-chorm.maxlen * legend.width / 20 , chorm.maxlen),
# round(seq(band - width/5, (length(chr.num) * band + band) * legend.height / 2 , length=maxbin.num+1), 2),
# t(matrix(0 : maxbin.num)), col=c("white", rev(heat.colors(maxbin.num))), add=TRUE)
legend.y <- round(seq(0, maxbin.num, length=legend.len))
len <- legend.y[2]
legend.y <- seq(0, maxbin.num, len)
if(!is.null(legend.max)){
if(legend.max < Maxbin.num){
if(!maxbin.num %in% legend.y){
legend.y <- c(legend.y, paste(">=", maxbin.num, sep=""))
legend.y.col <- c(legend.y[c(-1, -length(legend.y))], maxbin.num)
}else{
legend.y[length(legend.y)] <- paste(">=", maxbin.num, sep="")
legend.y.col <- c(legend.y[c(-1, -length(legend.y))], maxbin.num)
}
}else{
if(!maxbin.num %in% legend.y){
legend.y <- c(legend.y, maxbin.num)
}
legend.y.col <- c(legend.y[-1])
}
}else{
if(!maxbin.num %in% legend.y){
legend.y <- c(legend.y, paste(">", max(legend.y), sep=""))
legend.y.col <- c(legend.y[c(-1, -length(legend.y))], maxbin.num)
}else{
legend.y.col <- c(legend.y[-1])
}
}
legend.y.col <- as.numeric(legend.y.col)
legend.col <- c("grey", col[round(legend.y.col * length(col) / maxbin.num)])
if(plot) legend(x=(chorm.maxlen + chorm.maxlen/100), y=( -width/2.5 - band * (length(chr.num) - length(chr.num) - 1)), title="", legend=legend.y, pch=15, pt.cex = legend.pt.cex, col=legend.col,
cex=legend.cex, bty="n", y.intersp=legend.y.intersp, x.intersp=legend.x.intersp, yjust=0, xjust=0, xpd=TRUE)
if(!plot) return(list(den.col=col.seg, legend.col=legend.col, legend.y=legend.y))
}
GAPIT.Circle.Manhatton.Plot <- function(
Pmap,
col=c("#377EB8", "#4DAF4A", "#984EA3", "#FF7F00"),
#col=c("darkgreen", "darkblue", "darkyellow", "darkred"),
bin.size=1e6,
bin.max=NULL,
pch=19,
band=1,
cir.band=0.5,
H=1.5,
ylim=NULL,
cex.axis=1,
plot.type="c",
multracks=TRUE,
cex=c(0.5,0.8,1),
r=0.3,
xlab="Chromosome",
ylab=expression(-log[10](italic(p))),
xaxs="i",
yaxs="r",
outward=TRUE,
threshold = 0.01,
threshold.col="red",
threshold.lwd=1,
threshold.lty=2,
amplify= TRUE, # is that available for remark signal pch col
chr.labels=NULL,
signal.cex = 2,
signal.pch = 8,
signal.col="red",
signal.line=NULL,
cir.chr=TRUE,
cir.chr.h=1.3,
chr.den.col=c("darkgreen", "yellow", "red"),
#chr.den.col=c(126,177,153),
cir.legend=TRUE,
cir.legend.cex=0.8,
cir.legend.col="grey45",
LOG10=TRUE,
box=FALSE,
conf.int.col="grey",
file.output=TRUE,
file="pdf",
dpi=300,
xz=NULL,
memo=""
)
{ #print("Starting Circular-Manhattan plot!",quote=F)
taxa=colnames(Pmap)[-c(1:3)]
if(!is.null(memo) && memo != "") memo <- paste("_", memo, sep="")
if(length(taxa) == 0) taxa <- "Index"
taxa <- paste(taxa, memo, sep="")
col=rep(c( '#FF6A6A', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(length(taxa)/5))
legend.bit=round(nrow(Pmap)/30)
numeric.chr <- as.numeric(Pmap[, 1])
options(warn = 0)
max.chr <- max(numeric.chr, na.rm=TRUE)
aa=Pmap[1:legend.bit,]
aa[,2]=max.chr+1
#print(aa[,3])
aa[,3]=sample(1:10^7.5,legend.bit)
aa[,-c(1:3)]=0
Pmap=rbind(Pmap,aa)
#print(unique(Pmap[,2]))
#SNP-Density plot
if("d" %in% plot.type){
print("SNP_Density Plotting...")
if(file.output){
if(file=="jpg") jpeg(paste("SNP_Density.",paste(taxa,collapse="."),".jpg",sep=""), width = 9*dpi,height=7*dpi,res=dpi,quality = 100)
if(file=="pdf") pdf(paste("GAPIT.", taxa,".SNP_Density.Plot.pdf" ,sep=""), width = 9,height=7)
if(file=="tiff") tiff(paste("SNP_Density.",paste(taxa,collapse="."),".tiff",sep=""), width = 9*dpi,height=7*dpi,res=dpi)
par(xpd=TRUE)
}else{
if(is.null(dev.list())) dev.new(width = 9,height=7)
par(xpd=TRUE)
}
Densitplot(map=Pmap[,c(1:3)], col=col, bin=bin.size, legend.max=bin.max, main=paste("The number of SNPs within ", bin.size/1e6, "Mb window size", sep=""))
if(file.output) dev.off()
}
if(length(plot.type) !=1 | (!"d" %in% plot.type)){
#order Pmap by the name of SNP
#Pmap=Pmap[order(Pmap[,1]),]
Pmap <- as.matrix(Pmap)
#delete the column of SNPs names
Pmap <- Pmap[,-1]
Pmap[is.na(Pmap)]=1
#print(dim(Pmap))
#scale and adjust the parameters
cir.chr.h <- cir.chr.h/5
cir.band <- cir.band/5
threshold=threshold/nrow(Pmap)
if(!is.null(threshold)){
threshold.col <- rep(threshold.col,length(threshold))
threshold.lwd <- rep(threshold.lwd,length(threshold))
threshold.lty <- rep(threshold.lty,length(threshold))
signal.col <- rep(signal.col,length(threshold))
signal.pch <- rep(signal.pch,length(threshold))
signal.cex <- rep(signal.cex,length(threshold))
}
if(length(cex)!=3) cex <- rep(cex,3)
if(!is.null(ylim)){
if(length(ylim)==1) ylim <- c(0,ylim)
}
if(is.null(conf.int.col)) conf.int.col <- NA
if(is.na(conf.int.col)){
conf.int=FALSE
}else{
conf.int=TRUE
}
#get the number of traits
R=ncol(Pmap)-2
#replace the non-euchromosome
options(warn = -1)
numeric.chr <- as.numeric(Pmap[, 1])
options(warn = 0)
max.chr <- max(numeric.chr, na.rm=TRUE)
if(is.infinite(max.chr)) max.chr <- 0
map.xy.index <- which(!numeric.chr %in% c(0:max.chr))
if(length(map.xy.index) != 0){
chr.xy <- unique(Pmap[map.xy.index, 1])
for(i in 1:length(chr.xy)){
Pmap[Pmap[, 1] == chr.xy[i], 1] <- max.chr + i
}
}
Pmap <- matrix(as.numeric(Pmap), nrow(Pmap))
#order the GWAS results by chromosome and position
Pmap <- Pmap[order(Pmap[, 1], Pmap[,2]), ]
#get the index of chromosome
chr <- unique(Pmap[,1])
chr.ori <- chr
if(length(map.xy.index) != 0){
for(i in 1:length(chr.xy)){
chr.ori[chr.ori == max.chr + i] <- chr.xy[i]
}
}
pvalueT <- as.matrix(Pmap[,-c(1:2)])
#print(dim(pvalueT))
pvalue.pos <- Pmap[, 2]
p0.index <- Pmap[, 1] == 0
if(sum(p0.index) != 0){
pvalue.pos[p0.index] <- 1:sum(p0.index)
}
pvalue.pos.list <- tapply(pvalue.pos, Pmap[, 1], list)
#scale the space parameter between chromosomes
if(!missing(band)){
band <- floor(band*(sum(sapply(pvalue.pos.list, max))/100))
}else{
band <- floor((sum(sapply(pvalue.pos.list, max))/100))
}
if(band==0) band=1
if(LOG10){
pvalueT[pvalueT <= 0] <- 1
pvalueT[pvalueT > 1] <- 1
}
#set the colors for the plot
#palette(heat.colors(1024)) #(heatmap)
#T=floor(1024/max(pvalue))
#plot(pvalue,pch=19,cex=0.6,col=(1024-floor(pvalue*T)))
#print(col)
if(is.vector(col)){
col <- matrix(col,R,length(col),byrow=TRUE)
}
if(is.matrix(col)){
#try to transform the colors into matrix for all traits
col <- matrix(as.vector(t(col)),R,dim(col)[2],byrow=TRUE)
}
Num <- as.numeric(table(Pmap[,1]))
Nchr <- length(Num)
N <- NULL
#print(Nchr)
#set the colors for each traits
for(i in 1:R){
colx <- col[i,]
colx <- colx[!is.na(colx)]
N[i] <- ceiling(Nchr/length(colx))
}
#insert the space into chromosomes and return the midpoint of each chromosome
ticks <- NULL
pvalue.posN <- NULL
#pvalue <- pvalueT[,j]
for(i in 0:(Nchr-1)){
if (i==0){
#pvalue <- append(pvalue,rep(Inf,band),after=0)
pvalue.posN <- pvalue.pos.list[[i+1]] + band
ticks[i+1] <- max(pvalue.posN)-floor(max(pvalue.pos.list[[i+1]])/2)
}else{
#pvalue <- append(pvalue,rep(Inf,band),after=sum(Num[1:i])+i*band)
pvalue.posN <- c(pvalue.posN, max(pvalue.posN) + band + pvalue.pos.list[[i+1]])
ticks[i+1] <- max(pvalue.posN)-floor(max(pvalue.pos.list[[i+1]])/2)
}
}
pvalue.posN.list <- tapply(pvalue.posN, Pmap[, 1], list)
#NewP[[j]] <- pvalue
#merge the pvalues of traits by column
if(LOG10){
logpvalueT <- -log10(pvalueT)
}else{
pvalueT <- abs(pvalueT)
logpvalueT <- pvalueT
}
add <- list()
for(i in 1:R){
colx <- col[i,]
colx <- colx[!is.na(colx)]
add[[i]] <- c(Num,rep(0,N[i]*length(colx)-Nchr))
}
TotalN <- max(pvalue.posN)
if(length(chr.den.col) > 1){
cir.density=TRUE
den.fold <- 20
density.list <- Densitplot(map=Pmap[,c(1,1,2)], col=chr.den.col, plot=FALSE, bin=bin.size, legend.max=bin.max)
#list(den.col=col.seg, legend.col=legend.col, legend.y=legend.y)
}else{
cir.density=FALSE
}
#print(dim(pvalueT))
if(is.null(xz)){
signal.line.index <- NULL
if(!is.null(threshold)){
if(!is.null(signal.line)){
for(l in 1:R){
if(LOG10){
signal.line.index <- c(signal.line.index,which(pvalueT[,l] < min(threshold)))
}else{
signal.line.index <- c(signal.line.index,which(pvalueT[,l] > max(threshold)))
}
}
signal.line.index <- unique(signal.line.index)
}
}
signal.lty=rep(2,length(signal.line.index))
}else{
signal.line.index=as.numeric(as.vector(xz[,1]))
signal.lty=as.numeric(as.vector(xz[,2]))
}#end is.null(xz)
signal.line.index <- pvalue.posN[signal.line.index]
}
if("c" %in% plot.type)
{
if(file.output){
if(file=="jpg") jpeg(paste("Circular-Manhattan.",paste(taxa,collapse="."),".jpg",sep=""), width = 8*dpi,height=8*dpi,res=dpi,quality = 100)
if(file=="pdf") pdf(paste("GAPIT.", taxa,".Circular.Manhattan.Plot.pdf" ,sep=""), width = 10,height=10)
if(file=="tiff") tiff(paste("Circular-Manhattan.",paste(taxa,collapse="."),".tiff",sep=""), width = 8*dpi,height=8*dpi,res=dpi)
}
if(!file.output){
if(!is.null(dev.list())) dev.new(width=8, height=8)
par(pty="s", xpd=TRUE, mar=c(1,1,1,1))
}
par(pty="s", xpd=TRUE, mar=c(1,1,1,1))
RR <- r+H*R+cir.band*R
if(cir.density){
plot(NULL,xlim=c(1.05*(-RR-4*cir.chr.h),1.1*(RR+4*cir.chr.h)),ylim=c(1.05*(-RR-4*cir.chr.h),1.1*(RR+4*cir.chr.h)),axes=FALSE,xlab="",ylab="")
}else{
plot(NULL,xlim=c(1.05*(-RR-4*cir.chr.h),1.05*(RR+4*cir.chr.h)),ylim=c(1.05*(-RR-4*cir.chr.h),1.05*(RR+4*cir.chr.h)),axes=FALSE,xlab="",ylab="")
}
if(!is.null(signal.line)){
if(!is.null(signal.line.index)){
X1chr <- (RR)*sin(2*pi*(signal.line.index-round(band/2))/TotalN)
Y1chr <- (RR)*cos(2*pi*(signal.line.index-round(band/2))/TotalN)
X2chr <- (r)*sin(2*pi*(signal.line.index-round(band/2))/TotalN)
Y2chr <- (r)*cos(2*pi*(signal.line.index-round(band/2))/TotalN)
#print(signal.line)
#print(dim(pvalueT))
#print(head(pvalueT))
#print(dim(xz))
#print(xz)
#print(head(pvalue.posN))
segments(X1chr,Y1chr,X2chr,Y2chr,lty=signal.lty,lwd=signal.line,col="grey")
}
}
for(i in 1:R){
#get the colors for each trait
colx <- col[i,]
colx <- colx[!is.na(colx)]
#debug
#print(colx)
#print(paste("Circular_Manhattan Plotting ",taxa[i],"...",sep=""))
pvalue <- pvalueT[,i]
logpvalue <- logpvalueT[,i]
if(is.null(ylim)){
if(LOG10){
Max <- ceiling(-log10(min(pvalue[pvalue!=0])))
}else{
Max <- ceiling(max(pvalue[pvalue!=Inf]))
if(Max<=1)
Max <- max(pvalue[pvalue!=Inf])
}
}else{
Max <- ylim[2]
}
Cpvalue <- (H*logpvalue/Max)
if(outward==TRUE){
if(cir.chr==TRUE){
#plot the boundary which represents the chromosomes
polygon.num <- 1000
#print(length(chr))
for(k in 1:length(chr)){
if(k==1){
polygon.index <- seq(round(band/2)+1,-round(band/2)+max(pvalue.posN.list[[1]]), length=polygon.num)
#change the axis from right angle into circle format
X1chr=(RR)*sin(2*pi*(polygon.index)/TotalN)
Y1chr=(RR)*cos(2*pi*(polygon.index)/TotalN)
X2chr=(RR+cir.chr.h)*sin(2*pi*(polygon.index)/TotalN)
Y2chr=(RR+cir.chr.h)*cos(2*pi*(polygon.index)/TotalN)
#print(length(X1chr))
if(is.null(chr.den.col)){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=rep(colx,ceiling(length(chr)/length(colx)))[k],border=rep(colx,ceiling(length(chr)/length(colx)))[k])
}else{
if(cir.density){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col="grey",border="grey")
}else{
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=chr.den.col,border=chr.den.col)
}
}
}else{
polygon.index <- seq(1+round(band/2)+max(pvalue.posN.list[[k-1]]),-round(band/2)+max(pvalue.posN.list[[k]]), length=polygon.num)
X1chr=(RR)*sin(2*pi*(polygon.index)/TotalN)
Y1chr=(RR)*cos(2*pi*(polygon.index)/TotalN)
X2chr=(RR+cir.chr.h)*sin(2*pi*(polygon.index)/TotalN)
Y2chr=(RR+cir.chr.h)*cos(2*pi*(polygon.index)/TotalN)
if(is.null(chr.den.col)){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=rep(colx,ceiling(length(chr)/length(colx)))[k],border=rep(colx,ceiling(length(chr)/length(colx)))[k])
}else{
if(cir.density){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col="grey",border="grey")
}else{
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=chr.den.col,border=chr.den.col)
}
}
}
}
if(cir.density){
segments(
(RR)*sin(2*pi*(pvalue.posN-round(band/2))/TotalN),
(RR)*cos(2*pi*(pvalue.posN-round(band/2))/TotalN),
(RR+cir.chr.h)*sin(2*pi*(pvalue.posN-round(band/2))/TotalN),
(RR+cir.chr.h)*cos(2*pi*(pvalue.posN-round(band/2))/TotalN),
col=density.list$den.col, lwd=0.1
)
legend(
x=RR+4*cir.chr.h,
y=(RR+4*cir.chr.h)/2,
horiz=F,
title="Density", legend=density.list$legend.y, pch=15, pt.cex = 3, col=density.list$legend.col,
cex=1, bty="n",
y.intersp=1,
x.intersp=1,
yjust=0.5, xjust=0, xpd=TRUE
)
}
# XLine=(RR+cir.chr.h)*sin(2*pi*(1:TotalN)/TotalN)
# YLine=(RR+cir.chr.h)*cos(2*pi*(1:TotalN)/TotalN)
# lines(XLine,YLine,lwd=1.5)
if(cir.density){
circle.plot(myr=RR+cir.chr.h,lwd=1.5,add=TRUE,col='grey')
circle.plot(myr=RR,lwd=1.5,add=TRUE,col='grey')
}else{
circle.plot(myr=RR+cir.chr.h,lwd=1.5,add=TRUE)
circle.plot(myr=RR,lwd=1.5,add=TRUE)
}
}
#plot the y axis of legend for each trait
if(cir.legend==TRUE){
#try to get the number after radix point
if(Max<=1) {
round.n=nchar(as.character(10^(-ceiling(-log10(Max)))))-1
}else{
round.n=1
}
segments(0,r+H*(i-1)+cir.band*(i-1),0,r+H*i+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
segments(0,r+H*(i-1)+cir.band*(i-1),H/20,r+H*(i-1)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-1)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.75)+cir.band*(i-1),H/20,r+H*(i-0.75)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.75)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.5)+cir.band*(i-1),H/20,r+H*(i-0.5)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.5)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.25)+cir.band*(i-1),H/20,r+H*(i-0.25)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.25)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0)+cir.band*(i-1),H/20,r+H*(i-0)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
#text(-r/15,r+H*(i-0.75)+cir.band*(i-1),round(Max*0.25,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
text(-r/15,r+H*(i-0.5)+cir.band*(i-1),round(Max*0.5,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
text(-r/15,r+H*(i-0.25)+cir.band*(i-1),round(Max*0.75,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
#text(-r/15,r+H*(i-0)+cir.band*(i-1),round(Max*1,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
#text(r/5,0.4*(i-1),taxa[i],adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
}
X=(Cpvalue+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(pvalue.posN-round(band/2))/TotalN)
Y=(Cpvalue+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(pvalue.posN-round(band/2))/TotalN)
# plot point in figure
points(X[1:(length(X)-legend.bit)],Y[1:(length(Y)-legend.bit)],pch=19,cex=cex[1],col=rep(rep(colx,N[i]),add[[i]]))
# plot significant line
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
for(thr in 1:length(threshold)){
significantline1=ifelse(LOG10, H*(-log10(threshold[thr]))/Max, H*(threshold[thr])/Max)
#s1X=(significantline1+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(0:TotalN)/TotalN)
#s1Y=(significantline1+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(0:TotalN)/TotalN)
# plot significant line
if(significantline1<H){
#lines(s1X,s1Y,type="l",col=threshold.col,lwd=threshold.col,lty=threshold.lty)
#if(thr==length(threshold))circle.plot(myr=(significantline1+r+H*(i-1)+cir.band*(i-1)),col="black",lwd=threshold.lwd[thr],lty=threshold.lty[thr])
#print("!!!!!")
circle.plot(myr=(significantline1+r+H*(i-1)+cir.band*(i-1)),col=threshold.col[thr],lwd=threshold.lwd[thr],lty=threshold.lty[thr])
#circle.plot(myr=(significantline1+r+H*(i-1)+cir.band*(i-1)),col="black",lwd=threshold.lwd[thr],lty=threshold.lty[thr])
}else{
warning(paste("No significant points for ",taxa[i]," pass the threshold level using threshold=",threshold[thr],"!",sep=""))
}
}
}
}
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
if(amplify==TRUE){
if(LOG10){
threshold <- sort(threshold)
significantline1=H*(-log10(max(threshold)))/Max
}else{
threshold <- sort(threshold, decreasing=TRUE)
significantline1=H*(min(threshold))/Max
}
p_amp.index <- which(Cpvalue>=significantline1)
HX1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
#cover the points that exceed the threshold with the color "white"
points(HX1,HY1,pch=19,cex=cex[1],col="white")
for(ll in 1:length(threshold)){
if(ll == 1){
if(LOG10){
significantline1=H*(-log10(threshold[ll]))/Max
}else{
significantline1=H*(threshold[ll])/Max
}
p_amp.index <- which(Cpvalue>=significantline1)
HX1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
}else{
if(LOG10){
significantline0=H*(-log10(threshold[ll-1]))/Max
significantline1=H*(-log10(threshold[ll]))/Max
}else{
significantline0=H*(threshold[ll-1])/Max
significantline1=H*(threshold[ll])/Max
}
p_amp.index <- which(Cpvalue>=significantline1 & Cpvalue < significantline0)
HX1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
}
if(is.null(signal.col)){
# print(signal.pch)
points(HX1,HY1,pch=signal.pch,cex=signal.cex[ll]*cex[1],col=rep(rep(colx,N[i]),add[[i]])[p_amp.index])
}else{
# print(signal.pch)
points(HX1,HY1,pch=signal.pch,cex=signal.cex[ll]*cex[1],col=signal.col[ll])
}
}
}
}
}
if(cir.chr==TRUE){
ticks1=1.07*(RR+cir.chr.h)*sin(2*pi*(ticks-round(band/2))/TotalN)
ticks2=1.07*(RR+cir.chr.h)*cos(2*pi*(ticks-round(band/2))/TotalN)
if(is.null(chr.labels)){
#print(length(ticks))
for(i in 1:(length(ticks)-1)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.ori[i],srt=angle,font=2,cex=cex.axis)
}
}else{
for(i in 1:length(ticks)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.labels[i],srt=angle,font=2,cex=cex.axis)
}
}
}else{
ticks1=(0.9*r)*sin(2*pi*(ticks-round(band/2))/TotalN)
ticks2=(0.9*r)*cos(2*pi*(ticks-round(band/2))/TotalN)
if(is.null(chr.labels)){
for(i in 1:length(ticks)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.ori[i],srt=angle,font=2,cex=cex.axis)
}
}else{
for(i in 1:length(ticks)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.labels[i],srt=angle,font=2,cex=cex.axis)
}
}
}
}
if(outward==FALSE){
if(cir.chr==TRUE){
# XLine=(2*cir.band+RR+cir.chr.h)*sin(2*pi*(1:TotalN)/TotalN)
# YLine=(2*cir.band+RR+cir.chr.h)*cos(2*pi*(1:TotalN)/TotalN)
# lines(XLine,YLine,lwd=1.5)
polygon.num <- 1000
for(k in 1:length(chr)){
if(k==1){
polygon.index <- seq(round(band/2)+1,-round(band/2)+max(pvalue.posN.list[[1]]), length=polygon.num)
X1chr=(2*cir.band+RR)*sin(2*pi*(polygon.index)/TotalN)
Y1chr=(2*cir.band+RR)*cos(2*pi*(polygon.index)/TotalN)
X2chr=(2*cir.band+RR+cir.chr.h)*sin(2*pi*(polygon.index)/TotalN)
Y2chr=(2*cir.band+RR+cir.chr.h)*cos(2*pi*(polygon.index)/TotalN)
if(is.null(chr.den.col)){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=rep(colx,ceiling(length(chr)/length(colx)))[k],border=rep(colx,ceiling(length(chr)/length(colx)))[k])
}else{
if(cir.density){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col="grey",border="grey")
}else{
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=chr.den.col,border=chr.den.col)
}
}
}else{
polygon.index <- seq(1+round(band/2)+max(pvalue.posN.list[[k-1]]),-round(band/2)+max(pvalue.posN.list[[k]]), length=polygon.num)
X1chr=(2*cir.band+RR)*sin(2*pi*(polygon.index)/TotalN)
Y1chr=(2*cir.band+RR)*cos(2*pi*(polygon.index)/TotalN)
X2chr=(2*cir.band+RR+cir.chr.h)*sin(2*pi*(polygon.index)/TotalN)
Y2chr=(2*cir.band+RR+cir.chr.h)*cos(2*pi*(polygon.index)/TotalN)
if(is.null(chr.den.col)){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=rep(colx,ceiling(length(chr)/length(colx)))[k],border=rep(colx,ceiling(length(chr)/length(colx)))[k])
}else{
if(cir.density){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col="grey",border="grey")
}else{
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=chr.den.col,border=chr.den.col)
}
}
}
}
if(cir.density){
segments(
(2*cir.band+RR)*sin(2*pi*(pvalue.posN-round(band/2))/TotalN),
(2*cir.band+RR)*cos(2*pi*(pvalue.posN-round(band/2))/TotalN),
(2*cir.band+RR+cir.chr.h)*sin(2*pi*(pvalue.posN-round(band/2))/TotalN),
(2*cir.band+RR+cir.chr.h)*cos(2*pi*(pvalue.posN-round(band/2))/TotalN),
col=density.list$den.col, lwd=0.1
)
legend(
x=RR+4*cir.chr.h,
y=(RR+4*cir.chr.h)/2,
title="Density", legend=density.list$legend.y, pch=15, pt.cex = 3, col=density.list$legend.col,
cex=1, bty="n",
y.intersp=1,
x.intersp=1,
yjust=0.5, xjust=0, xpd=TRUE
)
}
if(cir.density){
circle.plot(myr=2*cir.band+RR+cir.chr.h,lwd=1.5,add=TRUE,col='grey')
circle.plot(myr=2*cir.band+RR,lwd=1.5,add=TRUE,col='grey')
}else{
circle.plot(myr=2*cir.band+RR+cir.chr.h,lwd=1.5,add=TRUE)
circle.plot(myr=2*cir.band+RR,lwd=1.5,add=TRUE)
}
}
if(cir.legend==TRUE){
#try to get the number after radix point
if(Max<=1) {
round.n=nchar(as.character(10^(-ceiling(-log10(Max)))))-1
}else{
round.n=2
}
segments(0,r+H*(i-1)+cir.band*(i-1),0,r+H*i+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
segments(0,r+H*(i-1)+cir.band*(i-1),H/20,r+H*(i-1)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-1)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.75)+cir.band*(i-1),H/20,r+H*(i-0.75)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.75)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.5)+cir.band*(i-1),H/20,r+H*(i-0.5)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.5)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.25)+cir.band*(i-1),H/20,r+H*(i-0.25)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.25)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0)+cir.band*(i-1),H/20,r+H*(i-0)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
text(-r/15,r+H*(i-0.25)+cir.band*(i-1),round(Max*0.25,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
#text(-r/15,r+H*(i-0.5)+cir.band*(i-1),round(Max*0.5,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
text(-r/15,r+H*(i-0.75)+cir.band*(i-1),round(Max*0.75,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
#text(-r/15,r+H*(i-1)+cir.band*(i-1),round(Max*1,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
#text(r,0.4*(i-1),taxa[i],adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
}
X=(-Cpvalue+r+H*i+cir.band*(i-1))*sin(2*pi*(pvalue.posN-round(band/2))/TotalN)
Y=(-Cpvalue+r+H*i+cir.band*(i-1))*cos(2*pi*(pvalue.posN-round(band/2))/TotalN)
#points(X,Y,pch=19,cex=cex[1],col=rep(rep(colx,N[i]),add[[i]]))
points(X[1:(length(X)-legend.bit)],Y[1:(length(Y)-legend.bit)],pch=19,cex=cex[1],col=rep(rep(colx,N[i]),add[[i]]))
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
for(thr in 1:length(threshold)){
significantline1=ifelse(LOG10, H*(-log10(threshold[thr]))/Max, H*(threshold[thr])/Max)
#s1X=(significantline1+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(0:TotalN)/TotalN)
#s1Y=(significantline1+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(0:TotalN)/TotalN)
if(significantline1<H){
#lines(s1X,s1Y,type="l",col=threshold.col,lwd=threshold.col,lty=threshold.lty)
circle.plot(myr=(-significantline1+r+H*i+cir.band*(i-1)),col=threshold.col[thr],lwd=threshold.lwd[thr],lty=threshold.lty[thr])
}else{
warning(paste("No significant points for ",taxa[i]," pass the threshold level using threshold=",threshold[thr],"!",sep=""))
}
}
if(amplify==TRUE){
if(LOG10){
threshold <- sort(threshold)
significantline1=H*(-log10(max(threshold)))/Max
}else{
threshold <- sort(threshold, decreasing=TRUE)
significantline1=H*(min(threshold))/Max
}
p_amp.index <- which(Cpvalue>=significantline1)
HX1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
#cover the points that exceed the threshold with the color "white"
points(HX1,HY1,pch=19,cex=cex[1],col="white")
for(ll in 1:length(threshold)){
if(ll == 1){
if(LOG10){
significantline1=H*(-log10(threshold[ll]))/Max
}else{
significantline1=H*(threshold[ll])/Max
}
p_amp.index <- which(Cpvalue>=significantline1)
HX1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
}else{
if(LOG10){
significantline0=H*(-log10(threshold[ll-1]))/Max
significantline1=H*(-log10(threshold[ll]))/Max
}else{
significantline0=H*(threshold[ll-1])/Max
significantline1=H*(threshold[ll])/Max
}
p_amp.index <- which(Cpvalue>=significantline1 & Cpvalue < significantline0)
HX1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
}
if(is.null(signal.col)){
points(HX1,HY1,pch=signal.pch,cex=signal.cex[ll]*cex[1],col=rep(rep(colx,N[i]),add[[i]])[p_amp.index])
}else{
points(HX1,HY1,pch=signal.pch,cex=signal.cex[ll]*cex[1],col=signal.col[ll])
}
}
}
}
}
if(cir.chr==TRUE){
ticks1=1.1*(2*cir.band+RR)*sin(2*pi*(ticks-round(band/2))/TotalN)
ticks2=1.1*(2*cir.band+RR)*cos(2*pi*(ticks-round(band/2))/TotalN)
if(is.null(chr.labels)){
for(i in 1:(length(ticks)-1)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.ori[i],srt=angle,font=2,cex=cex.axis)
}
}else{
for(i in 1:length(ticks)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.labels[i],srt=angle,font=2,cex=cex.axis)
}
}
}else{
ticks1=1.0*(RR+cir.band)*sin(2*pi*(ticks-round(band/2))/TotalN)
ticks2=1.0*(RR+cir.band)*cos(2*pi*(ticks-round(band/2))/TotalN)
if(is.null(chr.labels)){
for(i in 1:length(ticks)){
#adjust the angle of labels of circle plot
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.ori[i],srt=angle,font=2,cex=cex.axis)
}
}else{
for(i in 1:length(ticks)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.labels[i],srt=angle,font=2,cex=cex.axis)
}
}
}
}
}
taxa=append("Centre",taxa,)
taxa_col=rep("black",R)
taxa_col=append("red",taxa_col)
for(j in 1:(R+1)){
text(r/5,0.4*(j-1),taxa[j],adj=1,col=taxa_col[j],cex=cir.legend.cex,font=2)
}
taxa=taxa[-1]
if(file.output) dev.off()
}
if("q" %in% plot.type){
#print("Starting QQ-plot!",quote=F)
amplify=FALSE
if(multracks){
if(file.output){
if(file=="jpg") jpeg(paste("Multracks.QQ_plot.",paste(taxa,collapse="."),".jpg",sep=""), width = R*2.5*dpi,height=5.5*dpi,res=dpi,quality = 100)
if(file=="pdf") pdf(paste("Multracks.QQ_plot.",paste(taxa,collapse="."),".pdf",sep=""), width = R*2.5,height=5.5)
if(file=="tiff") tiff(paste("Multracks.QQ_plot.",paste(taxa,collapse="."),".tiff",sep=""), width = R*2.5*dpi,height=5.5*dpi,res=dpi)
par(mfcol=c(1,R),mar = c(0,1,4,1.5),oma=c(3,5,0,0),xpd=TRUE)
}else{
if(is.null(dev.list())) dev.new(width = 2.5*R, height = 5.5)
par(xpd=TRUE)
}
for(i in 1:R){
print(paste("Multracks_QQ Plotting ",taxa[i],"...",sep=""))
P.values=as.numeric(Pmap[,i+2])
P.values=P.values[!is.na(P.values)]
if(LOG10){
P.values=P.values[P.values>0]
P.values=P.values[P.values<=1]
N=length(P.values)
P.values=P.values[order(P.values)]
}else{
N=length(P.values)
P.values=P.values[order(P.values,decreasing=TRUE)]
}
p_value_quantiles=(1:length(P.values))/(length(P.values)+1)
log.Quantiles <- -log10(p_value_quantiles)
if(LOG10){
log.P.values <- -log10(P.values)
}else{
log.P.values <- P.values
}
#calculate the confidence interval of QQ-plot
if(conf.int){
N1=length(log.Quantiles)
c95 <- rep(NA,N1)
c05 <- rep(NA,N1)
for(j in 1:N1){
xi=ceiling((10^-log.Quantiles[j])*N)
if(xi==0)xi=1
c95[j] <- qbeta(0.95,xi,N-xi+1)
c05[j] <- qbeta(0.05,xi,N-xi+1)
}
index=length(c95):1
}else{
c05 <- 1
c95 <- 1
}
YlimMax <- max(floor(max(max(-log10(c05)), max(-log10(c95)))+1), floor(max(log.P.values)+1))
plot(NULL, xlim = c(0,floor(max(log.Quantiles)+1)), axes=FALSE, cex.axis=cex.axis, cex.lab=1.2,ylim=c(0,YlimMax),xlab ="", ylab="", main = taxa[i])
axis(1, at=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), labels=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), cex.axis=cex.axis)
axis(2, at=seq(0,YlimMax,ceiling(YlimMax/10)), labels=seq(0,YlimMax,ceiling(YlimMax/10)), cex.axis=cex.axis)
#plot the confidence interval of QQ-plot
if(conf.int) polygon(c(log.Quantiles[index],log.Quantiles),c(-log10(c05)[index],-log10(c95)),col=conf.int.col,border=conf.int.col)
if(!is.null(threshold.col)){par(xpd=FALSE); abline(a = 0, b = 1, col = threshold.col[1],lwd=2); par(xpd=TRUE)}
points(log.Quantiles, log.P.values, col = col[1],pch=1,cex=cex[3])
#print(max(log.Quantiles))
# print(length(log.Quantiles))
# print(length(log.P.values))
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
thre.line=-log10(min(threshold))
if(amplify==TRUE){
thre.index=which(log.P.values>=thre.line)
if(length(thre.index)!=0){
#cover the points that exceed the threshold with the color "white"
points(log.Quantiles[thre.index],log.P.values[thre.index], col = "white",pch=19,cex=cex[3])
if(is.null(signal.col)){
points(log.Quantiles[thre.index],log.P.values[thre.index],col = col[1],pch=signal.pch[1],cex=signal.cex[1])
}else{
points(log.Quantiles[thre.index],log.P.values[thre.index],col = signal.col[1],pch=signal.pch[1],cex=signal.cex[1])
}
}
}
}
}
}
if(box) box()
if(file.output) dev.off()
if(R > 1){
#qq_col=rainbow(R)
qq_col=rep(c( '#FF6A6A', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(R/5))
signal.col <- NULL
if(file.output){
if(file=="jpg") jpeg(paste("Multiple.QQ_plot.",paste(taxa,collapse="."),".jpg",sep=""), width = 5.5*dpi,height=5.5*dpi,res=dpi,quality = 100)
if(file=="pdf") pdf(paste("Multiple.QQ_plot.",paste(taxa,collapse="."),".pdf",sep=""), width = 5.5,height=5.5)
if(file=="tiff") tiff(paste("Multiple.QQ_plot.",paste(taxa,collapse="."),".tiff",sep=""), width = 5.5*dpi,height=5.5*dpi,res=dpi)
par(mar = c(5,5,4,2),xpd=TRUE)
}else{
dev.new(width = 5.5, height = 5.5)
par(xpd=TRUE)
}
P.values=as.numeric(Pmap[,i+2])
P.values=P.values[!is.na(P.values)]
if(LOG10){
P.values=P.values[P.values>0]
P.values=P.values[P.values<=1]
N=length(P.values)
P.values=P.values[order(P.values)]
}else{
N=length(P.values)
P.values=P.values[order(P.values,decreasing=TRUE)]
}
p_value_quantiles=(1:length(P.values))/(length(P.values)+1)
log.Quantiles <- -log10(p_value_quantiles)
# calculate the confidence interval of QQ-plot
if(conf.int){
N1=length(log.Quantiles)
c95 <- rep(NA,N1)
c05 <- rep(NA,N1)
for(j in 1:N1){
xi=ceiling((10^-log.Quantiles[j])*N)
if(xi==0)xi=1
c95[j] <- qbeta(0.95,xi,N-xi+1)
c05[j] <- qbeta(0.05,xi,N-xi+1)
}
index=length(c95):1
}
if(!conf.int){c05 <- 1; c95 <- 1}
Pmap.min <- Pmap[,3:(R+2)]
YlimMax <- max(floor(max(max(-log10(c05)), max(-log10(c95)))+1), -log10(min(Pmap.min[Pmap.min > 0])))
plot(NULL, xlim = c(0,floor(max(log.Quantiles)+1)), axes=FALSE, cex.axis=cex.axis, cex.lab=1.2,ylim=c(0, floor(YlimMax+1)),xlab =expression(Expected~~-log[10](italic(p))), ylab = expression(Observed~~-log[10](italic(p))), main = "QQ plot")
#legend("topleft",taxa,col=t(col)[1:R],pch=1,pt.lwd=2,text.font=6,box.col=NA)
legend("topleft",taxa,col=qq_col[1:R],pch=1,pt.lwd=3,text.font=6,box.col=NA)
axis(1, at=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), labels=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), cex.axis=cex.axis)
axis(2, at=seq(0,floor(YlimMax+1),ceiling((YlimMax+1)/10)), labels=seq(0,floor((YlimMax+1)),ceiling((YlimMax+1)/10)), cex.axis=cex.axis)
#print(log.Quantiles[index])
#print(index)
#print(length(log.Quantiles))
# plot the confidence interval of QQ-plot
if(conf.int) polygon(c(log.Quantiles[index],log.Quantiles),c(-log10(c05)[index],-log10(c95)),col=conf.int.col,border=conf.int.col)
for(i in 1:R){
#print(paste("Multraits_QQ Plotting ",taxa[i],"...",sep=""))
P.values=as.numeric(Pmap[,i+2])
P.values=P.values[!is.na(P.values)]
if(LOG10){
P.values=P.values[P.values>0]
P.values=P.values[P.values<=1]
N=length(P.values)
P.values=P.values[order(P.values)]
}else{
N=length(P.values)
P.values=P.values[order(P.values,decreasing=TRUE)]
}
p_value_quantiles=(1:length(P.values))/(length(P.values)+1)
log.Quantiles <- -log10(p_value_quantiles)
if(LOG10){
log.P.values <- -log10(P.values)
}else{
log.P.values <- P.values
}
if((i == 1) & !is.null(threshold.col)){par(xpd=FALSE); abline(a = 0, b = 1, col = threshold.col[1],lwd=2); par(xpd=TRUE)}
#print(length(log.Quantiles))
#print("!!!!!")
#points(log.Quantiles, log.P.values, col = t(col)[i],pch=1,lwd=3,cex=cex[3])
points(log.Quantiles, log.P.values, col = qq_col[i],pch=1,lwd=3,cex=cex[3])
#print(max(log.Quantiles))
#
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
thre.line=-log10(min(threshold))
if(amplify==TRUE){
thre.index=which(log.P.values>=thre.line)
if(length(thre.index)!=0){
# cover the points that exceed the threshold with the color "white"
points(log.Quantiles[thre.index],log.P.values[thre.index], col = "white",pch=19,lwd=3,cex=cex[3])
if(is.null(signal.col)){
points(log.Quantiles[thre.index],log.P.values[thre.index],col = t(col)[i],pch=signal.pch[1],cex=signal.cex[1])
}else{
points(log.Quantiles[thre.index],log.P.values[thre.index],col = signal.col[1],pch=signal.pch[1],cex=signal.cex[1])
}
}
}
}
}
}
box()
if(file.output) dev.off()
}
}else{
for(i in 1:R){
print(paste("Q_Q Plotting ",taxa[i],"...",sep=""))
if(file.output){
if(file=="jpg") jpeg(paste("QQplot.",taxa[i],".jpg",sep=""), width = 5.5*dpi,height=5.5*dpi,res=dpi,quality = 100)
if(file=="pdf") pdf(paste("QQplot.",taxa[i],".pdf",sep=""), width = 5.5,height=5.5)
if(file=="tiff") tiff(paste("QQplot.",taxa[i],".tiff",sep=""), width = 5.5*dpi,height=5.5*dpi,res=dpi)
par(mar = c(5,5,4,2),xpd=TRUE)
}else{
if(is.null(dev.list())) dev.new(width = 5.5, height = 5.5)
par(xpd=TRUE)
}
P.values=as.numeric(Pmap[,i+2])
P.values=P.values[!is.na(P.values)]
if(LOG10){
P.values=P.values[P.values>0]
P.values=P.values[P.values<=1]
N=length(P.values)
P.values=P.values[order(P.values)]
}else{
N=length(P.values)
P.values=P.values[order(P.values,decreasing=TRUE)]
}
p_value_quantiles=(1:length(P.values))/(length(P.values)+1)
log.Quantiles <- -log10(p_value_quantiles)
if(LOG10){
log.P.values <- -log10(P.values)
}else{
log.P.values <- P.values
}
#calculate the confidence interval of QQ-plot
if(conf.int){
N1=length(log.Quantiles)
c95 <- rep(NA,N1)
c05 <- rep(NA,N1)
for(j in 1:N1){
xi=ceiling((10^-log.Quantiles[j])*N)
if(xi==0)xi=1
c95[j] <- qbeta(0.95,xi,N-xi+1)
c05[j] <- qbeta(0.05,xi,N-xi+1)
}
index=length(c95):1
}else{
c05 <- 1
c95 <- 1
}
#print(max(log.Quantiles))
#print("@@@@@")
YlimMax <- max(floor(max(max(-log10(c05)), max(-log10(c95)))+1), floor(max(log.P.values)+1))
plot(NULL, xlim = c(0,floor(max(log.Quantiles)+1)), axes=FALSE, cex.axis=cex.axis, cex.lab=1.2,ylim=c(0,YlimMax),xlab =expression(Expected~~-log[10](italic(p))), ylab = expression(Observed~~-log[10](italic(p))), main = paste("QQplot of",taxa[i]))
axis(1, at=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), labels=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), cex.axis=cex.axis)
axis(2, at=seq(0,YlimMax,ceiling(YlimMax/10)), labels=seq(0,YlimMax,ceiling(YlimMax/10)), cex.axis=cex.axis)
#plot the confidence interval of QQ-plot
#print(log.Quantiles[index])
qq_col=rainbow(R)
#if(conf.int) polygon(c(log.Quantiles[index],log.Quantiles),c(-log10(c05)[index],-log10(c95)),col=conf.int.col,border=conf.int.col)
if(conf.int) polygon(c(log.Quantiles[index],log.Quantiles),c(-log10(c05)[index],-log10(c95)),col=qq_col[i],border=conf.int.col)
if(!is.null(threshold.col)){par(xpd=FALSE); abline(a = 0, b = 1, col = threshold.col[1],lwd=2); par(xpd=TRUE)}
points(log.Quantiles, log.P.values, col = col[1],pch=19,cex=2)
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
thre.line=-log10(min(threshold))
if(amplify==TRUE){
thre.index=which(log.P.values>=thre.line)
if(length(thre.index)!=0){
#print("!!!!")
#cover the points that exceed the threshold with the color "white"
points(log.Quantiles[thre.index],log.P.values[thre.index], col = "white",pch=19,lwd=3,cex=cex[3])
if(is.null(signal.col)){
points(log.Quantiles[thre.index],log.P.values[thre.index],col = col[1],pch=signal.pch[1],cex=signal.cex[1])
}else{
points(log.Quantiles[thre.index],log.P.values[thre.index],col = signal.col[1],pch=signal.pch[1],cex=signal.cex[1])
}
}
}
}
}
box()
if(file.output) dev.off()
}
}
print("Multiple QQ plot has been finished!",quote=F)
}
}#End of Whole function
#}
`GAPIT.Compress` <-
function(KI,kinship.cluster = "average",kinship.group = "Mean",GN=nrow(KI),Timmer,Memory){
#Object: To cluster individuals into groups based on kinship
#Output: GA, KG
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: April 14, 2011
##############################################################################################
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP start")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp start")
# Extract the line names
line.names <- KI[,1]
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Does this change memory0")
Memory=GAPIT.Memory(Memory=Memory,Infor="Does this change memory0")
# Remove the first column of the kinship matrix, which is the line names
KI <- KI[ ,-1]
# Convert kinship to distance
#distance.matrix <- 2 - KI
#distance.matrix.as.dist <- as.dist(distance.matrix)
#distance.matrix.as.dist <- as.dist(2 - KI)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP distance")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp distance")
#print(paste("The value of kinship.cluster is ", kinship.cluster, sep = ""))
# hclust() will perform the hiearchical cluster analysis
#cluster.distance.matrix <- hclust(distance.matrix.as.dist, method = kinship.cluster)
#cluster.distance.matrix <- hclust(as.dist(2 - KI), method = kinship.cluster)
distance.matrix=dist(KI,upper=TRUE) #Jiabo Wang modified ,the dist is right function for cluster
cluster.distance.matrix=hclust(distance.matrix,method=kinship.cluster)
#cutree(out_hclust,k=3)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP cluster")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp cluster")
# Cutree will assign lines into k clusters
group.membership <- cutree(cluster.distance.matrix, k = GN)
compress_z=table(group.membership,paste(line.names)) #build compress z with group.membership
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP cutree")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp cutree")
#calculate group kinship
if(kinship.group == "Mean"){
#This matrix ooperation is much faster than tapply function for "Mean"
x=as.factor(group.membership)
#b = model.matrix(~x-1)
n=max(as.numeric(as.vector(x)))
b=diag(n)[x,]
KG=t(b)%*%as.matrix(KI)%*%b
CT=t(b)%*%(0*as.matrix(KI)+1)%*%b
KG=as.matrix(KG/CT)
rownames(KG)=c(1:nrow(KG))
colnames(KG)=c(1:ncol(KG))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP calculation original")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp calculation original")
}else{
gm=as.factor(group.membership)
kv=as.numeric(as.matrix(KI))
kvr=rep(gm,ncol(KI))
kvc=as.numeric(t(matrix(kvr,nrow(KI),ncol(KI))))
kInCol=t(rbind(kv,kvr,kvc))
rm(gm)
rm(kv)
rm(kvr)
rm(kvc)
rm(KI)
gc()
#This part does not work yet
#if(kinship.group == "Mean")
# KG<- tapply(kInCol[,1], list(kInCol[,2], kInCol[,3]), mean)
if(kinship.group == "Max")
KG <- tapply(kInCol[,1], list(kInCol[,2], kInCol[,3]), max)
if(kinship.group == "Min")
KG <- tapply(kInCol[,1], list(kInCol[,2], kInCol[,3]), min)
if(kinship.group == "Median")
KG <- tapply(kInCol[,1], list(kInCol[,2], kInCol[,3]), median)
} #this is end of brancing "Mean" and the rest
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP calculation")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp calculation")
# add line names
#GA <- data.frame(group.membership)
GA <- data.frame(cbind(as.character(line.names),as.numeric(group.membership) ))
#Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP Final")
#Memory=GAPIT.Memory(Memory=Memory,Infor="CP Final")
#write.table(KG, paste("KG_from_", kinship.group, "_Method.txt"), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
#print("GAPIT.Compress accomplished successfully!")
return(list(GA=GA, KG=KG,Timmer=Timmer,Memory=Memory))
}#The function GAPIT.Compress ends here
#=============================================================================================
`GAPIT.Compression.Visualization` <-
function(Compression = Compression, name.of.trait = name.of.trait){
#Object: Conduct the Benjamini-Hochberg FDR-Controlling Procedure
#Output: Three pdfs: One of the log likelihood function, one of the genetic and error variance component,
# and one of the heritabilities
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: May 10, 2011
##############################################################################################
#Graph the optimum compression
print("GAPIT.Compression.Visualization")
#print(Compression)
if(length(Compression)<=6) Compression=t(as.matrix(Compression[which(Compression[,4]!="NULL" | Compression[,4]!="NaN"),]))
if(length(Compression)==6) Compression=matrix(Compression,1,6)
#print("Compression matrix")
#print(Compression)
#print(length(Compression) )
if(length(Compression)>6) Compression=Compression[which(Compression[,4]!="NULL" | Compression[,4]!="NaN"),]
if(length(Compression)<1) return() #no result
#Pie chart for the optimum setting
#-------------------------------------------------------------------------------
print("Pie chart")
LL=as.numeric(Compression[,4])
Compression.best=Compression[1,]
variance=as.numeric(Compression.best[5:6])
#colors <- c("grey50","grey70")
colors <- c("#990000","dimgray")
varp=variance/sum(variance)
h2.opt= varp[1]
labels0 <- round(varp * 100, 1)
labels <- paste(labels0, "%", sep="")
legend0=c("Genetic: ","Residual: ")
legend <- paste(legend0, round(variance*100)/100, sep="")
LL.best0=as.numeric(Compression.best[4] )
LL.best=paste("-2LL: ",floor(LL.best0*100)/100,sep="")
label.comp=paste(c("Cluster method: ","Group method: ","Group number: "), Compression.best[c(1:3)], sep="")
theOptimum=c(label.comp,LL.best)
#print(variance)
pdf(paste("GAPIT.", name.of.trait,".Optimum.pdf", sep = ""), width = 14)
par(mfrow = c(1,1), mar = c(1,1,5,5), lab = c(5,5,7))
pie(variance, col=colors, labels=labels,angle=45,border=NA)
legend(1.0, 0.5, legend, cex=1.5, bty="n",
fill=colors)
#Display the optimum compression
text(1.5,.0, "The optimum compression", col= "gray10")
for(i in 1:4){
text(1.5,-.1*i, theOptimum[i], col= "gray10")
}
dev.off()
#sort Compression by group number for plot order
Compression=Compression[order(as.numeric(Compression[,3])),]
#Graph compression with multiple groups
#print("Graph compression with multiple groups")
if(length(Compression)==6) return() #For to exit if only one row
#print("It should not go here")
if(length(unique(Compression[,3]))>1)
{
#Create a vector of colors
#print("Setting colors")
color.vector.basic <- c("red","blue","black", "blueviolet","indianred","cadetblue","orange")
color.vector.addition <- setdiff(c(colors()[grep("red",colors())], colors()[grep("blue",colors())]),color.vector.basic )
color.vector.addition.mixed <- sample(color.vector.addition,max(0,((length(unique(Compression[,1])) * length(unique(Compression[,2])))-length(color.vector.basic))))
color.vector <- c(color.vector.basic,color.vector.addition.mixed )
#Create a vector of numbers for the line dot types
line.vector <- rep(1:(length(unique(Compression[,1])) * length(unique(Compression[,2]))))
#We want to have a total of three plots, one displaying the likelihood function, one displaying the variance components, and one displaying the
# heritability
pdf(paste("GAPIT.", name.of.trait,".Compression.multiple.group", ".pdf", sep = ""), width = 14)
par(mfrow = c(2,3), mar = c(5,5,1,1), lab = c(5,5,7))
# Make the likelihood function plot
#print("Likelihood")
k <- 1
for(i in 1:length(unique(Compression[,1]))){
for(j in 1:length(unique(Compression[,2]))){
if((i == 1)&(j == 1)) {
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,4])
plot(y~x,type="l", pch = 30, lty = line.vector[i], ylim=c(min(as.numeric(Compression[,4])),max(as.numeric(Compression[,4]))), xlim = c(min(as.numeric(Compression[,3])),max(as.numeric(Compression[,3]))),
col = color.vector[j], xlab = "Number of Groups", ylab = "-2Log Likelihoood",lwd=1 )
label = paste(c(as.character(unique(Compression[,1]))[k]," ",as.character(unique(Compression[,2]))[j]), collapse = "")
}
if((i != 1)|(j != 1)) {
k <- k+1
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,4])
lines(y~x,type="l", pch = 30, lty = line.vector[i], col = color.vector[j])
label = c(label, paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = ""))
}
}
}
#Make a legend
#legend("topright", label, fill = color.vector)
legend.col= 1+floor(length(unique(Compression[,1])) * length(unique(Compression[,2]))/20)
line.style=rep(1:length(unique(Compression[,1])), each = length(unique(Compression[,2])))
line.color=rep(1:length(unique(Compression[,2])), length(unique(Compression[,1])))
legend("topright", label, col = color.vector[line.color], lty = line.style, ncol=legend.col,horiz=FALSE,bty="n")
# Make the genetic variance component plots
#print("genetic variance")
k <- 1
for(i in 1:length(unique(Compression[,1]))){
for(j in 1:length(unique(Compression[,2]))){
if((i == 1)&(j == 1)) {
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,5])
plot(y~x,type="l", pch = 17, lty = line.vector[i], ylim=c(min(as.numeric(Compression[,5])),max(as.numeric(Compression[,5]))), xlim = c(min(as.numeric(Compression[,3])),max(as.numeric(Compression[,3]))),
col = color.vector[j], xlab = "Number of Groups", ylab = "Genetic Variance", )
#label = paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = "")
}
if((i != 1)|(j != 1)) {
k <- k+1
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,5])
lines(y~x,type="l", pch = 17, lty = line.vector[i], col = color.vector[j])
#label = c(label, paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = ""))
}
}
}
#Make a legend
#legend("topleft", label, fill = color.vector)
# Make the residual variance component plots
k <- 1
for(i in 1:length(unique(Compression[,1]))){
for(j in 1:length(unique(Compression[,2]))){
if((i == 1)&(j == 1)) {
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,6])
plot(y~x,type="l", pch = 17, ylim=c(min(as.numeric(Compression[,6])),max(as.numeric(Compression[,6]))), xlim = c(min(as.numeric(Compression[,3])),max(as.numeric(Compression[,3]))),
col = color.vector[j], xlab = "Number of Groups", ylab = "Residual Variance", )
#label = paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = "")
}
if((i != 1)|(j != 1)) {
k <- k+1
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,6])
lines(y~x,type="l", pch = 17, lty = line.vector[i], col = color.vector[j])
#label = c(label, paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = ""))
}
}
}
#Make a legend
#legend("topright", label, fill = color.vector)
#calculate total variance and h2
#print("h2")
heritablilty.vector <- as.numeric(Compression[,5])/(as.numeric(Compression[,5]) + as.numeric(Compression[,6]))
totalVariance.vector <- as.numeric(as.numeric(Compression[,5]) + as.numeric(Compression[,6]))
Compression.h2 <- cbind(Compression, heritablilty.vector,totalVariance.vector)
# Make the total variance component plots
#print("Total variance")
k <- 1
for(i in 1:length(unique(Compression.h2[,1]))){
for(j in 1:length(unique(Compression.h2[,2]))){
if((i == 1)&(j == 1)) {
Compression.subset <- Compression.h2[which( (Compression.h2[,1] == as.character(unique(Compression.h2[,1])[i])) & (Compression.h2[,2] == as.character(unique(Compression.h2[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,8])
plot(y~x,type="l", pch = 17, lty = line.vector[k], ylim=c(min(as.numeric(Compression.h2[,8])),max(as.numeric(Compression.h2[,8]))), xlim = c(min(as.numeric(Compression.h2[,3])),max(as.numeric(Compression.h2[,3]))),
col = color.vector[1], xlab = "Number of Groups", ylab = "Total Variance", )
#label = paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = "")
}
if((i != 1)|(j != 1)) {
k <- k+1
Compression.subset <- Compression.h2[which( (Compression.h2[,1] == as.character(unique(Compression.h2[,1])[i])) & (Compression.h2[,2] == as.character(unique(Compression.h2[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,8])
lines(y~x,type="l", pch = 17, lty = line.vector[i], col = color.vector[j])
#label = c(label, paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = ""))
}
}
}
#Make a legend
#legend("topright", label, fill = color.vector)
# Make the heritability plots
#print("h2 plot")
k <- 1
for(i in 1:length(unique(Compression[,1]))){
for(j in 1:length(unique(Compression[,2]))){
if((i == 1)&(j == 1)) {
Compression.subset <- Compression.h2[which( (Compression.h2[,1] == as.character(unique(Compression.h2[,1])[i])) & (Compression.h2[,2] == as.character(unique(Compression.h2[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,7])
plot(y~x,type="l", pch = 17, lty = line.vector[k], ylim=c(min(as.numeric(Compression.h2[,7])),max(as.numeric(Compression.h2[,7]))), xlim = c(min(as.numeric(Compression.h2[,3])),max(as.numeric(Compression.h2[,3]))),
col = color.vector[1], xlab = "Number of Groups", ylab = "Heritability", )
#label = paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = "")
}
if((i != 1)|(j != 1)) {
k <- k+1
Compression.subset <- Compression.h2[which( (Compression.h2[,1] == as.character(unique(Compression.h2[,1])[i])) & (Compression.h2[,2] == as.character(unique(Compression.h2[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,7])
lines(y~x,type="l", lty = line.vector[i], pch = 17, col = color.vector[j])
#label = c(label, paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = ""))
}
}
}
#Make a legend
#legend("topleft", label, fill = color.vector)
legend.col= 1+floor(length(unique(Compression[,1])) * length(unique(Compression[,2]))/20)
line.style=rep(1:length(unique(Compression[,1])), each = length(unique(Compression[,2])))
line.color=rep(1:length(unique(Compression[,2])), length(unique(Compression[,1])))
# Make labels
plot(0~0,axes=FALSE,type="l",ylab = "",xlab = "",frame.plot=FALSE)
legend("topleft", label, col = color.vector[line.color], lty = line.style, ncol=legend.col,horiz=FALSE)
dev.off()
}#end of Graph compression with multiple groups
#Graph compression with single groups
#print("Graph compression with single groups")
if(length(unique(Compression[,3]))==1& length(unique(Compression[,1]))*length(unique(Compression[,2]))>1)
{
#Graph the compression with only one group
pdf(paste("GAPIT.Compression.single.group.", name.of.trait, ".pdf", sep = ""), width = 14)
par(mfrow = c(2,2), mar = c(5,5,1,1), lab = c(5,5,7))
nkt=length(unique(Compression[,1]))
nca=length(unique(Compression[,2]))
kvr=rep(c(1:nkt),nca)
kvc0=rep(c(1:nca),nkt)
kvc=as.numeric(t(matrix(kvc0,nca,nkt)))
kt.name=Compression[1:nkt,1]
ca.index=((1:nca)-1)*nkt+1
ca.name=Compression[ca.index,2]
KG<- t(tapply(as.numeric(Compression[,4]), list(kvr, kvc), mean))
colnames(KG)=kt.name
barplot(as.matrix(KG), ylab= "-2 Log Likelihood",beside=TRUE, col=rainbow(length(unique(Compression[,2]))))
KG<- t(tapply(as.numeric(Compression[,5]), list(kvr, kvc), mean))
colnames(KG)=kt.name
barplot(as.matrix(KG), ylab= "Genetic varaince", beside=TRUE, col=rainbow(length(unique(Compression[,2]))))
KG<- t(tapply(as.numeric(Compression[,6]), list(kvr, kvc), mean))
colnames(KG)=kt.name
barplot(as.matrix(KG), ylab= "Residual varaince", beside=TRUE, col=rainbow(length(unique(Compression[,2]))))
KG<- t(tapply(as.numeric(Compression[,5])/(as.numeric(Compression[,5])+as.numeric(Compression[,6])), list(kvr, kvc), mean))
colnames(KG)=kt.name
barplot(as.matrix(KG), ylab= "Heritability", beside=TRUE, col=rainbow(length(unique(Compression[,2]))),ylim=c(0,1))
legend("topleft", paste(t(ca.name)), cex=0.8,bty="n", fill=rainbow(length(unique(Compression[,2]))),horiz=TRUE)
dev.off()
} #end of Graph compression with single groups
print("GAPIT.Compression.Visualization accomplished successfully!")
#return(list(compression=Compression.h2,h2=h2.opt))
return
}#GAPIT.Compression.Plots ends here
#=============================================================================================
`GAPIT.Create.Indicator` <-
function(xs, SNP.impute = "Major" ){
#Object: To esimate variance component by using EMMA algorithm and perform GWAS with P3D/EMMAx
#Output: ps, REMLs, stats, dfs, vgs, ves, BLUP, BLUP_Plus_Mean, PEV
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: April 30, 2012
##############################################################################################
#Determine the number of bits of the genotype
bit=nchar(as.character(xs[1]))
#Identify the SNPs classified as missing
if(bit==1) {
xss[xss=="xs"]="N"
xs[xs=="-"]="N"
xs[xs=="+"]="N"
xs[xs=="/"]="N"
xs[xs=="K"]="Z" #K (for GT genotype)is is replaced by Z to ensure heterozygose has the largest value
}
if(bit==2) {
xs[xs=="xsxs"]="N"
xs[xs=="--"]="N"
xs[xs=="++"]="N"
xs[xs=="//"]="N"
xs[xs=="NN"]="N"
}
#Create the indicators
#Sort the SNPs by genotype frequency
xs.temp <- xs[-which(xs == "N")]
frequ<- NULL
for(i in 1:length(unique(xs.temp))) frequ <- c(frequ, length(which(xs == unique(xs)[i])))
unique.sorted <- cbind(unique(xs.temp), frequ)
print("unique.sorted is")
print(unique.sorted)
unique.sorted <- unique.sorted[order(unique.sorted[,2]),]
unique.sorted <- unique.sorted[,-2]
#Impute based on the major and minor allele frequencies
if(SNP.impute == "Major") xs[which(is.na(xs))] = unique.sorted[1]
if(SNP.impute == "Minor") xs[which(is.na(xs))] = unique.sorted[length(unique.sorted)]
if(SNP.impute == "Middle") xs[which(is.na(xs))] = unique.sorted[2]
x.ind <- NULL
for(i in unique.sorted){
x.col <- rep(NA, length(xs))
x.col[which(xs==i)] <- 1
x.col[which(xs!=i)] <- 0
x.ind <- cbind(x.ind,x.col)
}
return(x.ind)
print("GAPIT.Create.Indicator accomplished successfully!")
}#end of GAPIT.Create.Indicator function
#=============================================================================================
`GAPIT.DP` <-
function(G=NULL,GD=NULL,GM=NULL,KI=NULL,Z=NULL,CV=NULL,CV.Inheritance=NULL,GP=NULL,GK=NULL,
group.from=30 ,group.to=1000000,group.by=10,DPP=100000,
kinship.cluster="average", kinship.group='Mean',kinship.algorithm="VanRaden",
bin.from=10000,bin.to=10000,bin.by=10000,inclosure.from=10,inclosure.to=10,inclosure.by=10,
SNP.P3D=TRUE,SNP.effect="Add",SNP.impute="Middle",PCA.total=0, SNP.fraction = 1, seed = 123, BINS = 20,SNP.test=TRUE,
SNP.MAF=0,FDR.Rate = 1, SNP.FDR=1,SNP.permutation=FALSE,SNP.CV=NULL,SNP.robust="GLM", NJtree.group=NULL,NJtree.type=c("fan","unrooted"),plot.bin=10^6,PCA.col=NULL,PCA.3d=FALSE,
file.from=1, file.to=1, file.total=NULL, file.fragment = 99999,file.path=NULL,Inter.Plot=FALSE,Inter.type=c("m","q"),
file.G=NULL, file.Ext.G=NULL,file.GD=NULL, file.GM=NULL, file.Ext.GD=NULL,file.Ext.GM=NULL,
ngrid = 100, llim = -10, ulim = 10, esp = 1e-10, Multi_iter=FALSE,windowsize=5e9,
LD.chromosome=NULL,LD.location=NULL,LD.range=NULL, p.threshold=NA,QTN.threshold=0.01,maf.threshold=0.03,
sangwich.top=NULL,sangwich.bottom=NULL,QC=TRUE,GTindex=NULL,LD=0.1,
file.output=TRUE,cutOff=0.01, Model.selection = FALSE,output.numerical = FALSE,
output.hapmap = FALSE, Create.indicator = FALSE,QTN=NULL, QTN.round=1,QTN.limit=0, QTN.update=TRUE, QTN.method="Penalty", Major.allele.zero = FALSE,
method.GLM="fast.lm",method.sub="reward",method.sub.final="reward",method.bin="static",bin.size=c(1000000),bin.selection=c(10,20,50,100,200,500,1000),
memo="",Prior=NULL,ncpus=1,maxLoop=3,threshold.output=.01, WS=c(1e0,1e3,1e4,1e5,1e6,1e7),alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),maxOut=100,QTN.position=NULL,
converge=1,iteration.output=FALSE,acceleration=0,iteration.method="accum",PCA.View.output=TRUE,Geno.View.output=TRUE,plot.style="Oceanic",SUPER_GD=NULL,SUPER_GS=FALSE,CG=NULL,model="MLM"){
#Object: To Data and Parameters
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("GAPIT.DP in process...")
#Judge phenotype genotype and GAPIT logical
#print(file.from)
#print(kinship.algorithm)
#print(NJtree.group)
myGenotype<-GAPIT.Genotype(G=G,GD=GD,GM=GM,KI=KI,PCA.total=PCA.total,kinship.algorithm=kinship.algorithm,SNP.fraction=SNP.fraction,SNP.test=FALSE,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,
file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF=SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,NJtree.group=NJtree.group,NJtree.type=NJtree.type,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,
GP=GP,GK=GK,bin.size=NULL,inclosure.size=NULL,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,GTindex=NULL,file.output=file.output, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero,Geno.View.output=Geno.View.output,PCA.col=PCA.col,PCA.3d=PCA.3d)
# }
KI=myGenotype$KI
PC=myGenotype$PC
print(dim(PC))
genoFormat=myGenotype$genoFormat
hasGenotype=myGenotype$hasGenotype
byFile=myGenotype$byFile
fullGD=myGenotype$fullGD
GD=myGenotype$GD
GI=myGenotype$GI
GT=myGenotype$GT
G=myGenotype$G
chor_taxa=myGenotype$chor_taxa
#if G exist turn to GD and GM
if(output.numerical) write.table(GD, "GAPIT.Genotype.Numerical.txt", quote = FALSE, sep = "\t", row.names = TRUE,col.names = NA)
if(output.hapmap) write.table(myGenotype$G, "GAPIT.Genotype.hmp.txt", quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
rownames(GD)=GT
colnames(GD)=GI[,1]
GD=cbind(as.data.frame(GT),GD)
print("GAPIT.DP accomplished successfully for multiple traits. Results are saved")
return (list(Y=NULL,G=G,GD=GD,GM=GI,KI=KI,Z=Z,CV=CV,CV.Inheritance= CV.Inheritance,GP=GP,GK=GK,PC=PC,GI=GI,
group.from= group.from ,group.to= group.to,group.by= group.by,DPP= DPP, name.of.trait=NULL,
kinship.cluster= kinship.cluster, kinship.group= kinship.group,kinship.algorithm= kinship.algorithm,NJtree.group=NJtree.group,NJtree.type=NJtree.type,PCA.col=PCA.col,PCA.3d=PCA.3d,
bin.from= bin.from,bin.to= bin.to,bin.by= bin.by,inclosure.from= inclosure.from,inclosure.to= inclosure.to,inclosure.by= inclosure.by,
SNP.P3D= SNP.P3D,SNP.effect= SNP.effect,SNP.impute= SNP.impute,PCA.total= PCA.total, SNP.fraction = SNP.fraction, seed = seed,
BINS = BINS,SNP.test=SNP.test, SNP.MAF= SNP.MAF,FDR.Rate = FDR.Rate, SNP.FDR= SNP.FDR,SNP.permutation= SNP.permutation,
SNP.CV= SNP.CV,SNP.robust= SNP.robust, file.from= file.from, file.to=file.to, file.total= file.total, file.fragment = file.fragment,file.path= file.path,
file.G= file.G, file.Ext.G= file.Ext.G,file.GD= file.GD, file.GM= file.GM, file.Ext.GD= file.Ext.GD,file.Ext.GM= file.Ext.GM,
ngrid = ngrid, llim = llim, ulim = ulim, esp = esp,Inter.Plot=Inter.Plot,Inter.type=Inter.type,
LD.chromosome= LD.chromosome,LD.location= LD.location,LD.range= LD.range,Multi_iter=Multi_iter,
sangwich.top= sangwich.top,sangwich.bottom= sangwich.bottom,QC= QC,GTindex= GTindex,LD= LD,GT=GT,
file.output= file.output,cutOff=cutOff, Model.selection = Model.selection,output.numerical = output.numerical,
output.hapmap = output.hapmap, Create.indicator = Create.indicator,
QTN= QTN, QTN.round= QTN.round,QTN.limit= QTN.limit, QTN.update= QTN.update, QTN.method= QTN.method, Major.allele.zero = Major.allele.zero,
method.GLM= method.GLM,method.sub= method.sub,method.sub.final= method.sub.final,
method.bin= method.bin,bin.size= bin.size,bin.selection= bin.selection,
memo= memo,Prior= Prior,ncpus=1,maxLoop= maxLoop,threshold.output= threshold.output,
WS= WS,alpha= alpha,maxOut= maxOut,QTN.position= QTN.position, converge=1,iteration.output= iteration.output,acceleration=0,
iteration.method= iteration.method,PCA.View.output= PCA.View.output,
p.threshold=p.threshold,QTN.threshold=QTN.threshold,
maf.threshold=maf.threshold,chor_taxa=chor_taxa,windowsize=windowsize,
Geno.View.output= Geno.View.output,plot.style= plot.style,SUPER_GD= SUPER_GD,SUPER_GS= SUPER_GS,CG=CG,plot.bin=plot.bin))
} #end of GAPIT DP function
#=============================================================================================
`GAPIT.EMMAxP3D` <-
function(ys,xs,K=NULL,Z=NULL,X0=NULL,CVI=NULL,CV.Inheritance=NULL,GI=NULL,GP=NULL,
file.path=NULL,file.from=NULL,file.to=NULL,file.total=1, genoFormat="Hapmap", file.fragment=NULL,byFile=FALSE,fullGD=TRUE,SNP.fraction=1,
file.G=NULL,file.Ext.G=NULL,GTindex=NULL,file.GD=NULL, file.GM=NULL, file.Ext.GD=NULL,file.Ext.GM=NULL,
SNP.P3D=TRUE,Timmer,Memory,optOnly=TRUE,SNP.effect="Add",SNP.impute="Middle", SNP.permutation=FALSE,
ngrids=100,llim=-10,ulim=10,esp=1e-10,name.of.trait=NULL, Create.indicator = FALSE, Major.allele.zero = FALSE){
#Object: To esimate variance component by using EMMA algorithm and perform GWAS with P3D/EMMAx
#Output: ps, REMLs, stats, dfs, vgs, ves, BLUP, BLUP_Plus_Mean, PEV
#Authors: Feng Tian, Alex Lipka and Zhiwu Zhang
# Last update: April 6, 2016
# Library used: EMMA (Kang et al, Genetics, Vol. 178, 1709-1723, March 2008)
# Note: This function was modified from the function of emma.REML.t from the library
##############################################################################################
#print("EMMAxP3D started...")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="P3D Start")
Memory=GAPIT.Memory(Memory=Memory,Infor="P3D Start")
#When numeric genotypes are selected, impute the missing SNPs with the allele indicated by the "SNP.impute" value
if(!optOnly){
if(SNP.impute == "Major") xs[which(is.na(xs))] = 2
if(SNP.impute == "Minor") xs[which(is.na(xs))] = 0
if(SNP.impute == "Middle") xs[which(is.na(xs))] = 1
}
#--------------------------------------------------------------------------------------------------------------------<
#Change data to matrix format if they are not
if(is.null(dim(ys)) || ncol(ys) == 1) ys <- matrix(ys, 1, length(ys))
if(is.null(X0)) X0 <- matrix(1, ncol(ys), 1)
#handler of special Z and K
if(!is.null(Z)){ if(ncol(Z) == nrow(Z)) Z = NULL }
if(!is.null(K)) {if(length(K)<= 1) K = NULL}
#Extract dimension information
g <- nrow(ys) #number of traits
n <- ncol(ys) #number of observation
q0 <- ncol(X0)#number of fixed effects
q1 <- q0 + 1 #Nuber of fixed effect including SNP
nr=n
if(!is.null(K)) tv=ncol(K)
#decomposation without fixed effect
#print("Caling emma.eigen.L...")
if(!is.null(K)) eig.L <- emma.eigen.L(Z, K) #this function handle both NULL Z and non-NULL Z matrix
#eig.L$values[eig.L$values<0]=0
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="eig.L")
Memory=GAPIT.Memory(Memory=Memory,Infor="eig.L")
#decomposation with fixed effect (SNP not included)
#print("Calling emma.eigen.R.w.Z...")
X <- X0 #covariate variables such as population structure
if(!is.null(Z) & !is.null(K)) eig.R <- try(emma.eigen.R.w.Z(Z, K, X),silent=TRUE) #This will be used to get REstricted ML (REML)
if(is.null(Z) & !is.null(K)) eig.R <- try(emma.eigen.R.wo.Z( K, X),silent=TRUE) #This will be used to get REstricted ML (REML)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="eig.R")
Memory=GAPIT.Memory(Memory=Memory,Infor="eig.R")
#eig.R$values[eig.R$values<0]=0
#print(labels(eig.R))
#print(length(eig.R$values))
#print(dim(eig.R$vectors))
#print("emma.eigen.R.w.Z called!!!")
#Handler of error in emma
#print("!!!!!!")
if(!is.null(K)){
if(inherits(eig.R, "try-error"))
return(list(ps = NULL, REMLs = NA, stats = NULL, effect.est = NULL, dfs = NULL,maf=NULL,nobs = NULL,Timmer=Timmer,Memory=Memory,
vgs = NA, ves = NA, BLUP = NULL, BLUP_Plus_Mean = NULL,
PEV = NULL, BLUE=NULL))
#print("@@@@@")
}
#-------------------------------------------------------------------------------------------------------------------->
#print("Looping through traits...")
#Loop on Traits
for (j in 1:g)
{
if(optOnly){
#REMLE <- GAPIT.emma.REMLE(ys[j,], X, K, Z, ngrids, llim, ulim, esp, eig.R)
#vgs <- REMLE$vg
#ves <- REMLE$ve
#REMLs <- REMLE$REML
#REMLE_delta=REMLE$delta
if(!is.null(K)){
REMLE <- GAPIT.emma.REMLE(ys[j,], X, K, Z, ngrids, llim, ulim, esp, eig.R)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="REML")
Memory=GAPIT.Memory(Memory=Memory,Infor="REML")
rm(eig.R)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="eig.R removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="eig.R removed")
vgs <- REMLE$vg
ves <- REMLE$ve
REMLs <- REMLE$REML
REMLE_delta=REMLE$delta
rm(REMLE)
gc()
}
vids <- !is.na(ys[j,])
yv <- ys[j, vids]
if(!is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix(c(sqrt(1/(eig.L$values + REMLE_delta)),rep(sqrt(1/REMLE_delta),nr - tv)),nr,((nr-tv)+length(eig.L$values)),byrow=TRUE)
if( is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix( sqrt(1/(eig.L$values + REMLE_delta)),nr,length(eig.L$values),byrow=TRUE)
if( !is.null(Z) & !is.null(K)) eig.full.plus.delta <- as.matrix(c((eig.L$values + REMLE_delta), rep(REMLE_delta,(nr - tv))))
if( is.null(Z) & !is.null(K)) eig.full.plus.delta <- as.matrix((eig.L$values + REMLE_delta))
if(!is.null(K)){
if(length(which(eig.L$values < 0)) > 0 ){
#print("---------------------------------------------------The group kinship matrix at this compression level is not positive semidefinite. Please select another compression level.---------------------------------------------------")
#return(list(ps = NULL, REMLs = 999999, stats = NULL, effect.est = NULL, dfs = NULL,maf=NULL,nobs = NULL,Timmer=Timmer,Memory=Memory,
#vgs = 1.000, ves = 1.000, BLUP = NULL, BLUP_Plus_Mean = NULL,
#PEV = NULL, BLUE=NULL))
}
}
#Calculate the log likelihood function for the intercept only model
X.int <- matrix(1,nrow(as.matrix(yv)),ncol(as.matrix(yv)))
iX.intX.int <- solve(crossprod(X.int, X.int))
iX.intY <- crossprod(X.int, as.matrix(as.matrix(yv)))
beta.int <- crossprod(iX.intX.int, iX.intY) #Note: we can use crossprod here becase iXX is symmetric
X.int.beta.int <- X.int%*%beta.int
logL0 <- 0.5*((-length(yv))*log(((2*pi)/length(yv))
*crossprod((yv-X.int.beta.int),(yv-X.int.beta.int)))
-length(yv))
#print(paste("The value of logL0 inside of the optonly template is is",logL0, sep = ""))
#print(paste("The value of nrow(as.matrix(ys[!is.na(ys)])) is ",nrow(as.matrix(ys[!is.na(ys)])), sep = ""))
if(!is.null(K)){
yt <- yt <- crossprod(U, yv)
X0t <- crossprod(U, X0)
X0X0 <- crossprod(X0t, X0t)
X0Y <- crossprod(X0t,yt)
XY <- X0Y
iX0X0 <- try(solve(X0X0),silent=TRUE)
if(inherits(iX0X0, "try-error")){
iX0X0 <- ginv(X0X0)
print("At least two of your covariates are linearly dependent. Please reconsider the covariates you are using for GWAS and GPS")
}
iXX <- iX0X0
}
if(is.null(K)){
iXX <- try(solve(crossprod(X,X)),silent=TRUE)
if(inherits(iXX, "try-error"))iXX <- ginv(crossprod(X,X))
XY = crossprod(X,yv)
}
beta <- crossprod(iXX,XY) #Note: we can use crossprod here because iXX is symmetric
X.beta <- X%*%beta
beta.cv=beta
BLUE=X.beta
if(!is.null(K)){
U.times.yv.minus.X.beta <- crossprod(U,(yv-X.beta))
logLM <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta))
- sum(log(eig.full.plus.delta)) - length(yv))
}
if(is.null(K)){
U.times.yv.minus.X.beta <- yv-X.beta
logLM <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta)) - length(yv))
}
}#End if(optOnly)
#--------------------------------------------------------------------------------------------------------------------<
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Trait")
Memory=GAPIT.Memory(Memory=Memory,Infor="Trait")
if(!is.null(K)){
REMLE <- GAPIT.emma.REMLE(ys[j,], X, K, Z, ngrids, llim, ulim, esp, eig.R)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="REML")
Memory=GAPIT.Memory(Memory=Memory,Infor="REML")
rm(eig.R)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="eig.R removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="eig.R removed")
vgs <- REMLE$vg
ves <- REMLE$ve
REMLs <- REMLE$REML
REMLE_delta=REMLE$delta
rm(REMLE)
gc()
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="REMLE removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="REMLE removed")
if(!is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix(c(sqrt(1/(eig.L$values + REMLE_delta)),rep(sqrt(1/REMLE_delta),nr - tv)),nr,((nr-tv)+length(eig.L$values)),byrow=TRUE)
if( is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix( sqrt(1/(eig.L$values + REMLE_delta)),nr,length(eig.L$values),byrow=TRUE)
if( !is.null(Z) & !is.null(K)) eig.full.plus.delta <- as.matrix(c((eig.L$values + REMLE_delta), rep(REMLE_delta,(nr - tv))))
if( is.null(Z) & !is.null(K)) eig.full.plus.delta <- as.matrix((eig.L$values + REMLE_delta))
if(!is.null(K)){
if(length(which(eig.L$values < 0)) > 0 ){
#print("---------------------------------------------------The group kinship matrix at this compression level is not positive semidefinite. Please select another compression level.---------------------------------------------------")
#return(list(ps = NULL, REMLs = 999999, stats = NULL, effect.est = NULL, dfs = NULL,maf=NULL,nobs = NULL,Timmer=Timmer,Memory=Memory,
#vgs = 1.000, ves = 1.000, BLUP = NULL, BLUP_Plus_Mean = NULL,
#PEV = NULL, BLUE=NULL))
}
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="U Matrix")
Memory=GAPIT.Memory(Memory=Memory,Infor="U Matrix")
if(SNP.P3D == TRUE)rm(eig.L)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="eig.L removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="eig.L removed")
#-------------------------------------------------------------------------------------------------------------------->
#The cases that go though multiple file once
file.stop=file.to
if(optOnly) file.stop=file.from
if(fullGD) file.stop=file.from
if(!fullGD & !optOnly) {print("Screening SNPs from file...")}
#Add loop for genotype data files
for (file in file.from:file.stop)
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="New Genotype file")
Memory=GAPIT.Memory(Memory=Memory,Infor="New Genotype file")
frag=1
numSNP=file.fragment
myFRG=NULL
while(numSNP==file.fragment) { #this is problematic if the read end at the last line
#initial previous SNP storage
x.prev <- vector(length = 0)
#force to skip the while loop if optOnly
if(optOnly) numSNP=0
#Determine the case of first file and first fragment: skip read file
if(file==file.from & frag==1& SNP.fraction<1){
firstFileFirstFrag=TRUE
}else{
firstFileFirstFrag=FALSE
}
#In case of xs is not full GD, replace xs from file
if(!fullGD & !optOnly & !firstFileFirstFrag )
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Clean myFRG")
Memory=GAPIT.Memory(Memory=Memory,Infor="Clean myFRG")
#update xs for each file
rm(xs)
rm(myFRG)
gc()
print(paste("Current file: ",file," , Fragment: ",frag,sep=""))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Read file fragment")
Memory=GAPIT.Memory(Memory=Memory,Infor="Read file fragment")
myFRG=GAPIT.Fragment( file.path=file.path, file.total=file.total,file.G=file.G,file.Ext.G=file.Ext.G,
seed=seed,SNP.fraction=SNP.fraction,SNP.effect=SNP.effect,SNP.impute=SNP.impute,genoFormat=genoFormat,
file.GD=file.GD,file.Ext.GD=file.Ext.GD,file.GM=file.GM,file.Ext.GM=file.Ext.GM,file.fragment=file.fragment,file=file,frag=frag,
Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype file converted")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype file converted")
#print("-----------------------------------------------------------------")
if(is.null(myFRG$GD)){
xs=NULL
}else{
xs=myFRG$GD[GTindex,]
}
if(!is.null(myFRG$GI)) {
colnames(myFRG$GI)=c("SNP","Chromosome","Position")
GI=as.matrix(myFRG$GI)
}
if(!is.null(myFRG$GI)) {
numSNP=ncol(myFRG$GD)
} else{
numSNP=0
}
if(is.null(myFRG))numSNP=0 #force to end the while loop
} # end of if(!fullGD)
if(fullGD)numSNP=0 #force to end the while loop
#Skip REML if xs is from a empty fragment file
if(!is.null(xs)) {
if(is.null(dim(xs)) || nrow(xs) == 1) xs <- matrix(xs, length(xs),1)
xs <- as.matrix(xs)
if(length(which(is.na(xs)))>0){ #for the case where fragments are read in
if(SNP.impute == "Major") xs[which(is.na(xs))] = 2
if(SNP.impute == "Minor") xs[which(is.na(xs))] = 0
if(SNP.impute == "Middle") xs[which(is.na(xs))] = 1
}
m <- ncol(xs) #number of SNPs
t <- nrow(xs) #number of individuals
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before cleaning")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before cleaning")
#allocate spaces for SNPs
rm(dfs)
rm(stats)
rm(effect.est)
rm(ps)
rm(nobs)
rm(maf)
rm(rsquare_base)
rm(rsquare)
rm(df)
rm(tvalue)
rm(stderr)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="After cleaning")
Memory=GAPIT.Memory(Memory=Memory,Infor="After cleaning")
dfs <- matrix(nrow = m, ncol = g)
stats <- matrix(nrow = m, ncol = g)
if(!Create.indicator) effect.est <- matrix(nrow = m, ncol = g)
if(Create.indicator) effect.est <- NULL
ps <- matrix(nrow = m, ncol = g)
nobs <- matrix(nrow = m, ncol = g)
maf <- matrix(nrow = m, ncol = g)
rsquare_base <- matrix(nrow = m, ncol = g)
rsquare <- matrix(nrow = m, ncol = g)
df <- matrix(nrow = m, ncol = g)
tvalue <- matrix(nrow = m, ncol = g)
stderr <- matrix(nrow = m, ncol = g)
#print(paste("Memory allocated.",sep=""))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Memory allocation")
Memory=GAPIT.Memory(Memory=Memory,Infor="Memory allocation")
if(optOnly)mloop=0
if(!optOnly)mloop=m
#Loop on SNPs
#print(paste("Number of SNPs is ",mloop," in genotype file ",file, sep=""))
#set starting point of loop
if(file==file.from&frag==1){loopStart=0}else{loopStart=1}
for (i in loopStart:mloop){
#print(i)
#--------------------------------------------------------------------------------------------------------------------<
normalCase=TRUE
if((i >0)&(floor(i/1000)==i/1000)) {print(paste("Genotype file: ", file,", SNP: ",i," ",sep=""))}
# To extract current snp. It save computation for next one in case they are identical
if(i ==0&file==file.from&frag==1){
#For the model without fitting SNP
vids <- !is.na(ys[j,]) #### Feng changed
xv <- ys[j, vids]*0+1 #### Feng changed
}
if(i >0 | file>file.from | frag>1){
if(Create.indicator){ #I need create indicators and then calculate the minor allele frequency
condition.temp <- unique(xs[vids,i])
#Define what a bit is
bit=nchar(as.character(xs[vids[1],i]))
#Expand on the "which" statement below to include all instances of missing data
if(bit==1) condition <- condition.temp[-which(condition.temp == "N")]
if(bit==2) condition <- condition.temp[-which(condition.temp == "NN")]
#print("condition.temp is ")
#print(condition.temp)
#print("condition is")
#print(condition)
#print(paste("The value of i is ", i, sep = ""))
if(length(condition) <= 1){
dfs[i, ] <- rep(NA, g)
stats[i, ] <- rep(NA, g)
effect.est <- rbind(effect.est, c(i,rep(NA, g), rep(NA, g)))
ps[i, ] = rep(1, g)
rsquare[i, ] <- rep(NA,g)
rsquare_base[i, ]<-rep(NA,g)
maf[i, ] <- rep(0, g)
df[i, ] <- rep(NA,g)
tvalue[i, ] <- rep(NA,g)
stderr[i, ] <- rep(NA,g)
normalCase=FALSE
x.prev= vector(length = 0)
}
}
if(normalCase){
#print("The head of xs[vids,i] is")
#print(head(xs[vids,i]))
if(Create.indicator){ #I need create indicators and then calculate the minor allele frequency
indicator <- GAPIT.Create.Indicator(xs[vids,i], SNP.impute = SNP.impute)
xv <- indicator$x.ind
vids <- !is.na(xv[,1]) #### Feng changed
vids.TRUE=which(vids==TRUE)
vids.FALSE=which(vids==FALSE)
ns=nrow(xv)
ss=sum(xv[,ncol(xv)])
maf[i]=min(ss/ns,1-ss/ns)
nobs[i]=ns
q1 <- q0 + ncol(xv) # This is done so that parameter estimates for all indicator variables are included
#These two matrices need to be reinitiated for each SNP.
Xt <- matrix(NA,nr, q1)
iXX=matrix(NA,q1,q1)
}
}
if(!Create.indicator){ #### Feng changed
#print(xs[1:10,1:10])
xv <- xs[vids,i]
vids <- !is.na(xs[,i]) #### Feng changed
vids.TRUE=which(vids==TRUE)
vids.FALSE=which(vids==FALSE)
ns=length(xv)
#print(xv))
ss=sum(xv)
maf[i]=min(.5*ss/ns,1-.5*ss/ns)
nobs[i]=ns
}
nr <- sum(vids)
if(i ==1 & file==file.from&frag==1 & !Create.indicator) {
Xt <- matrix(NA,nr, q1)
iXX=matrix(NA,q1,q1)
}
}
#Situation of no variation for SNP except the fisrt one(synthetic for EMMAx/P3D)
if((min(xv) == max(xv)) & (i >0 | file>file.from |frag>1))
{
dfs[i, ] <- rep(NA, g)
stats[i, ] <- rep(NA, g)
if(!Create.indicator) effect.est[i,] <- rep(NA, g)
if(Create.indicator) effect.est <- rbind(effect.est, c(i,rep(NA, g),rep(NA, g)))
ps[i, ] = rep(1, g)
rsquare[i, ] <- rep(NA,g)
rsquare_base[i, ]<-rep(NA,g)
df[i, ] <- rep(NA,g)
tvalue[i, ] <- rep(NA,g)
stderr[i, ] <- rep(NA,g)
normalCase=FALSE
}else if(identical(x.prev, xv)) #Situation of the SNP is identical to previous
{
if(i >1 | file>file.from | frag>1){
dfs[i, ] <- dfs[i - 1, ]
stats[i, ] <- stats[i - 1, ]
if(!Create.indicator) effect.est[i, ] <- effect.est[i - 1, ]
if(Create.indicator) effect.est <- rbind(effect.est, c(i, rep(NA, g), rep(NA, g))) #If the previous SNP is idnetical, indicate this by "NA"
ps[i, ] <- ps[i - 1, ]
rsquare[i, ] <- rsquare[i - 1, ]
rsquare_base[i, ] <-rsquare_base[i - 1, ]
df[i, ] <- df[i - 1, ]
tvalue[i, ] <- tvalue[i - 1, ]
stderr[i, ] <- stderr[i - 1, ]
normalCase=FALSE
}
}
#-------------------------------------------------------------------------------------------------------------------->
if(i == 0 &file==file.from &frag==1){
#Calculate the log likelihood function for the intercept only model
#vids <- !is.na(ys[j,])
yv <- ys[j, vids]
X.int <- matrix(1,nrow(as.matrix(yv)),ncol(as.matrix(yv)))
iX.intX.int <- solve(crossprod(X.int, X.int))
iX.intY <- crossprod(X.int, as.matrix(as.matrix(yv)))
beta.int <- crossprod(iX.intX.int, iX.intY) #Note: we can use crossprod here becase iXX is symmetric
X.int.beta.int <- X.int%*%beta.int
#X.int <- matrix(1,nrow(as.matrix(ys[!is.na(ys)])),ncol(as.matrix(ys[!is.na(ys)])))
#iX.intX.int <- solve(crossprod(X.int, X.int))
#iX.intY <- crossprod(X.int, as.matrix(ys[!is.na(ys)]))
#beta.int <- crossprod(iX.intX.int, iX.intY) #Note: we can use crossprod here becase iXX is symmetric
#X.int.beta.int <- X.int%*%beta.int
logL0 <- 0.5*((-length(yv))*log(((2*pi)/length(yv))
*crossprod((yv-X.int.beta.int),(yv-X.int.beta.int)))
-length(yv))
#logL0 <- 0.5*((-nrow(as.matrix(ys[!is.na(ys)])))*log(((2*pi)/nrow(ys))
# *crossprod(((as.matrix(ys[!is.na(ys)]))-X.int.beta.int),((as.matrix(ys[!is.na(ys)]))-X.int.beta.int)))
# -nrow(as.matrix(ys[!is.na(ys)])))
#print(paste("The value of logL0 inside of the calculating SNPs loop is", logL0, sep = ""))
}
#Normal case
if(normalCase)
{
#--------------------------------------------------------------------------------------------------------------------<
#nv <- sum(vids)
yv <- ys[j, vids] #### Feng changed
nr <- sum(vids) #### Feng changed
if(!is.null(Z) & !is.null(K))
{
r<- ncol(Z) ####Feng, add a variable to indicate the number of random effect
vran <- vids[1:r] ###Feng, add a variable to indicate random effects with nonmissing genotype
tv <- sum(vran) #### Feng changed
}
#-------------------------------------------------------------------------------------------------------------------->
#--------------------------------------------------------------------------------------------------------------------<
if(i >0 | file>file.from|frag>1) dfs[i, j] <- nr - q1
if(i >0 | file>file.from|frag>1){
if(!Create.indicator) X <- cbind(X0[vids, , drop = FALSE], xs[vids,i])
if(Create.indicator){
X <- cbind(X0[vids, , drop = FALSE], xv)
#if(i == 1) {print("the head of X for running GWAS is")}
#if(i == 1) {print(head(X))}
}
}
#Recalculate eig and REML if not using P3D NOTE THIS USED TO BE BEFORE the two solid lines
if(SNP.P3D==FALSE & !is.null(K))
{
if(!is.null(Z)) eig.R <- emma.eigen.R.w.Z(Z, K, X) #This will be used to get REstricted ML (REML)
if(is.null(Z)) eig.R <- emma.eigen.R.wo.Z( K, X) #This will be used to get REstricted ML (REML)
if(!is.null(Z)) REMLE <- GAPIT.emma.REMLE(ys[j,], X, K, Z, ngrids, llim, ulim, esp, eig.R)
if(is.null(Z)) REMLE <- GAPIT.emma.REMLE(ys[j,], X, K, Z = NULL, ngrids, llim, ulim, esp, eig.R)
if(!is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix(c(sqrt(1/(eig.L$values + REMLE$delta)),rep(sqrt(1/REMLE$delta),nr - tv)),nr,((nr-tv)+length(eig.L$values)),byrow=TRUE)
if(is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix( sqrt(1/(eig.L$values + REMLE$delta)),nr,length(eig.L$values),byrow=TRUE)
vgs <- REMLE$vg
ves <- REMLE$ve
REMLs <- REMLE$REML
REMLE_delta=REMLE$delta
}
if(n==nr)
{
if(!is.null(K))
{
yt <- crossprod(U, yv)
if(i == 0 &file==file.from &frag==1){
X0t <- crossprod(U, X0)
Xt <- X0t
}
if(i > 0 | file>file.from |frag>1){
#if(i ==1 & file==file.from&frag==1) Xt <- matrix(NA,nr, q1)
if(Create.indicator){
xst <- crossprod(U, X[,(q0+1):q1])
Xt[1:nr,1:q0] <- X0t
Xt[1:nr,(q0+1):q1] <- xst
}
#print(paste("i:",i,"q0:",q0,"q1:",q1,"nt:",nr,"XT row",nrow(Xt),"XT col",ncol(Xt),sep=" "))
if(!Create.indicator){
xst <- crossprod(U, X[,ncol(X)])
Xt[1:nr,1:q0] <- X0t
Xt[1:nr,q1] <- xst
}
}
}else{
yt=yv
if(i == 0 &file==file.from &frag==1) X0t <- X0
if(i > 0 | file>file.from |frag>1) xst <- X[,ncol(X)]
}
if(i == 0 &file==file.from &frag==1){
X0X0 <- crossprod(X0t, X0t)
#XX <- X0X0
}
if(i > 0 | file>file.from |frag>1){
#if(i == 1)XX=matrix(NA,q1,q1)
X0Xst <- crossprod(X0t,xst)
XstX0 <- t(X0Xst)
xstxst <- crossprod(xst, xst)
# if(i == 1){
# Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Calculate_X0Xst_XstX0_xstxst")
# Memory=GAPIT.Memory(Memory=Memory,Infor="Calculate_X0Xst_XstX0_xstxst")
# }
#XX <- rbind(cbind(X0X0, X0Xst), cbind(XstX0, xstxst))
#XX[1:q0,1:q0] <- X0X0
#XX[q1,1:q0] <- X0Xst
#XX[1:q0,q1] <- X0Xst
#XX[q1,q1] <- xstxst
}
if(X0X0[1,1] == "NaN")
{
Xt[which(Xt=="NaN")]=0
yt[which(yt=="NaN")]=0
XX=crossprod(Xt, Xt)
}
if(i == 0 &file==file.from & frag==1){
X0Y <- crossprod(X0t,yt)
XY <- X0Y
}
if(i > 0 | file>file.from |frag>1){
xsY <- crossprod(xst,yt)
XY <- c(X0Y,xsY)
# if(i == 1){
# Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Calculate_xsY_X0Y")
# Memory=GAPIT.Memory(Memory=Memory,Infor="Calculate_xsY_X0Y")
# }
}
#XY = crossprod(Xt,yt)
}
#Missing SNP
if(n>nr)
{
UU=crossprod(U,U)
A11=UU[vids.TRUE,vids.TRUE]
A12=UU[vids.TRUE,vids.FALSE]
A21=UU[vids.FALSE,vids.TRUE]
A22=UU[vids.FALSE,vids.FALSE]
A22i =try(solve(A22),silent=TRUE )
if(inherits(A22i, "try-error")) A22i <- ginv(A22)
F11=A11-A12%*%A22i%*%A21
XX=crossprod(X,F11)%*%X
XY=crossprod(X,F11)%*%yv
}
if(i == 0 &file==file.from &frag==1){
iX0X0 <- try(solve(X0X0),silent=TRUE)
if(inherits(iX0X0, "try-error")){
iX0X0 <- ginv(X0X0)
print("At least two of your covariates are linearly dependent. Please reconsider the covariates you are using for GWAS and GPS")
}
iXX <- iX0X0
}
if(i > 0 | file>file.from |frag>1){
#if(i ==1 &file==file.from &frag==1) iXX=matrix(NA,q1,q1)
if(Create.indicator){
B22 <- xstxst - XstX0%*%iX0X0%*%X0Xst
invB22 <- solve(B22)
B21 <- tcrossprod(XstX0, iX0X0)
NeginvB22B21 <- crossprod(-invB22,B21)
B11 <- iX0X0 + as.numeric(invB22)*crossprod(B21,B21)
iXX[1:q0,1:q0]=B11
iXX[(q0+1):q1,(q0+1):q1]=solve(B22)
iXX[(q0+1):q1,1:q0]=NeginvB22B21
iXX[1:q0,(q0+1):q1]=t(NeginvB22B21)
}
if(!Create.indicator){
B22 <- xstxst - XstX0%*%iX0X0%*%X0Xst
invB22 <- 1/B22
#B12 <- crossprod(iX0X0,X0Xst)
B21 <- tcrossprod(XstX0, iX0X0)
NeginvB22B21 <- crossprod(-invB22,B21)
#B11 <- iX0X0 + B12%*%invB22%*%B21
B11 <- iX0X0 + as.numeric(invB22)*crossprod(B21,B21)
#iXX <- rbind(cbind(B11,t(NeginvB22B21)), cbind(NeginvB22B21,invB22))
iXX[1:q0,1:q0]=B11
iXX[q1,q1]=1/B22
iXX[q1,1:q0]=NeginvB22B21
iXX[1:q0,q1]=NeginvB22B21
}
#if(i == 1){
# Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Calculate_iXX")
# Memory=GAPIT.Memory(Memory=Memory,Infor="Calculate_iXX")
#}
}
if(is.null(K)){
iXX <- try(solve(crossprod(X,X)),silent=TRUE)
if(inherits(iXX, "try-error"))iXX <- ginv(crossprod(X,X))
XY = crossprod(X,yv)
}
#iXX <- try(solve(XX))
#if(inherits(iXX, "try-error")) iXX <- ginv(crossprod(Xt, Xt))
#print("The dimension if iXX is")
#print(dim(iXX))
#print("The length of XY is")
#print(length(XY))
beta <- crossprod(iXX,XY) #Note: we can use crossprod here becase iXX is symmetric
#print("beta was estimated")
#-------------------------------------------------------------------------------------------------------------------->
#--------------------------------------------------------------------------------------------------------------------<
if(i ==0 &file==file.from &frag==1 & !is.null(K))
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="ReducedModel")
Memory=GAPIT.Memory(Memory=Memory,Infor="ReducdModel")
#beta.cv=beta
XtimesBetaHat <- X%*%beta
YminusXtimesBetaHat <- ys[j,]- XtimesBetaHat
vgK <- vgs*K
Dt <- crossprod(U, YminusXtimesBetaHat)
if(!is.null(Z)) Zt <- crossprod(U, Z)
if(is.null(Z)) Zt <- t(U)
if(X0X0[1,1] == "NaN")
{
Dt[which(Dt=="NaN")]=0
Zt[which(Zt=="NaN")]=0
}
BLUP <- K %*% crossprod(Zt, Dt) #Using K instead of vgK because using H=V/Vg
#print("!!!!")
#Clean up the BLUP starf to save memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="before Dt clean")
Memory=GAPIT.Memory(Memory=Memory,Infor="before Dt clean")
rm(Dt)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Dt clean")
Memory=GAPIT.Memory(Memory=Memory,Infor="Dt clean")
grand.mean.vector <- rep(beta[1], length(BLUP))
BLUP_Plus_Mean <- grand.mean.vector + BLUP
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="BLUP")
Memory=GAPIT.Memory(Memory=Memory,Infor="BLUP")
#PEV
C11=try(vgs*solve(crossprod(Xt,Xt)),silent=TRUE)
if(inherits(C11, "try-error")) C11=vgs*ginv(crossprod(Xt,Xt))
C21=-K%*%crossprod(Zt,Xt)%*%C11
Kinv=try(solve(K) ,silent=TRUE )
if(inherits(Kinv, "try-error")) Kinv=ginv(K)
if(!is.null(Z)) term.0=crossprod(Z,Z)/ves
if(is.null(Z)) term.0=diag(1/ves,nrow(K))
term.1=try(solve(term.0+Kinv/vgs ) ,silent=TRUE )
if(inherits(term.1, "try-error")) term.1=ginv(term.0+Kinv/vgs )
term.2=C21%*%crossprod(Xt,Zt)%*%K
C22=(term.1-term.2 )
PEV=as.matrix(diag(C22))
#print(paste("The value of is.na(CVI) is", is.na(CVI), sep = ""))
if(!is.na(CVI)){
XCV=as.matrix(cbind(1,data.frame(CVI[,-1])))
#CV.Inheritance specified
beta.Inheritance=beta
if(!is.null(CV.Inheritance)){
XCV=XCV[,1:(1+CV.Inheritance)]
beta.Inheritance=beta[1:(1+CV.Inheritance)]
}
#Interception only
if(length(beta)==1)XCV=X
BLUE=try(XCV%*%beta.Inheritance,silent=TRUE)
if(inherits(BLUE, "try-error")) BLUE = NA
#print("GAPIT just after BLUE")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PEV")
Memory=GAPIT.Memory(Memory=Memory,Infor="PEV")
}#end of if(i ==0&file==file.from & !is.null(K))
if(is.na(CVI)) BLUE = NA
}#end if(!is.na(CVI))
#-------------------------------------------------------------------------------------------------------------------->
#--------------------------------------------------------------------------------------------------------------------<
if(i ==0 &file==file.from &frag==1 & is.null(K))
{
YY=crossprod(yt, yt)
ves=(YY-crossprod(beta,XY))/(n-q0)
r=yt-X%*%iXX%*%XY
REMLs=-.5*(n-q0)*log(det(ves)) -.5*n -.5*(n-q0)*log(2*pi)
# REMLs=-.5*n*log(det(ves)) -.5*log(det(iXX)/ves) -.5*crossprod(r,r)/ves -.5*(n-q0)*log(2*pi)
vgs = 0
BLUP = 0
BLUP_Plus_Mean = NaN
PEV = ves
#print(paste("X row:",nrow(X)," col:",ncol(X)," beta:",length(beta),sep=""))
XCV=as.matrix(cbind(1,data.frame(CVI[,-1])))
#CV.Inheritance specified
beta.Inheritance=beta
if(!is.null(CV.Inheritance)){
XCV=XCV[,1:(1+CV.Inheritance)]
beta.Inheritance=beta[1:(1+CV.Inheritance)]
}
#Interception only
if(length(beta)==1)XCV=X
#BLUE=XCV%*%beta.Inheritance modified by jiabo wang 2016.11.21
BLUE=try(XCV%*%beta.Inheritance,silent=TRUE)
if(inherits(BLUE, "try-error")) BLUE = NA
}
#Clean up the BLUP stuff to save memory
if(i ==0 &file==file.from &frag==1 & !is.null(K))
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="K normal")
Memory=GAPIT.Memory(Memory=Memory,Infor="K normal")
if(SNP.P3D == TRUE) K=1 #NOTE: When SNP.P3D == FALSE, this line will mess up the spectral decomposition of the kinship matrix at each SNP.
rm(Dt)
rm(Zt)
rm(Kinv)
rm(C11)
rm(C21)
rm(C22)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="K set to 1")
Memory=GAPIT.Memory(Memory=Memory,Infor="K set to 1")
}
if(i == 0 &file==file.from & frag==1){
beta.cv=beta
X.beta <- X%*%beta
if(!is.null(K)){
U.times.yv.minus.X.beta <- crossprod(U,(yv-X.beta))
logLM_Base <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta))
- sum(log(eig.full.plus.delta)) - length(yv))
}
if(is.null(K)){
U.times.yv.minus.X.beta <- yv-X.beta
logLM_Base <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta)) - length(yv))
}
rsquare_base_intitialized <- 1-exp(-(2/length(yv))*(logLM_Base-logL0))
}
#print(Create.indicator)
#calculate t statistics and P-values
if(i > 0 | file>file.from |frag>1)
{
if(!Create.indicator){
#if(i<5)print(beta[q1])
#if(i<5)print(iXX[q1, q1])
if(!is.null(K)) stats[i, j] <- beta[q1]/sqrt(iXX[q1, q1] *vgs)
if(is.null(K)) stats[i, j] <- beta[q1]/sqrt(iXX[q1, q1] *ves)
effect.est[i, ] <- beta[q1]
ps[i, ] <- 2 * pt(abs(stats[i, ]), dfs[i, ],lower.tail = FALSE)
if(is.na(ps[i,]))ps[i,]=1
#print(c(i,ps[i,],stats[i,],beta[q1],iXX[q1, q1]))
}
if(Create.indicator){
F.num.first.two <- crossprod(beta[(q0+1):q1], solve(iXX[(q0+1):q1,(q0+1):q1]))
if(!is.null(K)) stats[i, j] <- (F.num.first.two %*% beta[(q0+1):q1])/(length((q0+1):q1)*vgs)
if(is.null(K)) stats[i, j] <- (F.num.first.two %*% beta[(q0+1):q1])/(length((q0+1):q1)*ves)
effect.est <- rbind(effect.est, cbind(rep(i,length((q0+1):q1)), indicator$unique.SNPs, beta[(q0+1):q1])) #Replace with rbind
ps[i, ] <- pf(stats[i, j], df1=length((q0+1):q1), df2=(nr-ncol(X)), lower.tail = FALSE) #Alex, are these denominator degrees of freedom correct?
dfs[i,] <- nr-nrow(X)
}
#Calculate the maximum full likelihood function value and the r square
X.beta <- X%*%beta
if(!is.null(K)){
U.times.yv.minus.X.beta <- crossprod(U,(yv-X.beta))
logLM <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta))
- sum(log(eig.full.plus.delta))- length(yv))
}
if(is.null(K)){
U.times.yv.minus.X.beta <- yv-X.beta
logLM <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta)) - length(yv))
}
rsquare_base[i, ] <- rsquare_base_intitialized
rsquare[i, ] <- 1-exp(-(2/length(yv))*(logLM-logL0))
#Calculate df, t value and standard error _xiaolei changed
df[i,] <- dfs[i,]
tvalue[i,] <- stats[i, j]
stderr[i,] <- beta[ncol(CVI)+1]/stats[i, j]
#stderr[i,] <- sqrt(vgs)
# modified by Jiabo at 20191115
}
#print("!!!!!!!!!!!!!!!")
#print(Create.indicator)
#-------------------------------------------------------------------------------------------------------------------->
} # End of if(normalCase)
x.prev=xv #update SNP
} # End of loop on SNPs
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Screening SNPs")
Memory=GAPIT.Memory(Memory=Memory,Infor="Screening SNPs")
# print(head(tvalue))
# print(head(stderr))
# print(head(effect.est))
#output p value for the genotype file
if(!fullGD)
{
#print("!!!!!!!!!!")
#print(dim(GI))
write.table(GI, paste("GAPIT.TMP.GI.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = TRUE)
write.table(ps, paste("GAPIT.TMP.ps.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(maf, paste("GAPIT.TMP.maf.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(nobs, paste("GAPIT.TMP.nobs.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(rsquare_base, paste("GAPIT.TMP.rsquare.base.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(rsquare, paste("GAPIT.TMP.rsquare.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(df, paste("GAPIT.TMP.df.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(tvalue, paste("GAPIT.TMP.tvalue.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(stderr, paste("GAPIT.TMP.stderr.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(effect.est, paste("GAPIT.TMP.effect.est.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
#rm(dfs,stats,ps,nobs,maf,GI) #This cause problem on return
#gc()
}
frag=frag+1 #Progress to next fragment
} #end of if(!is.null(X))
} #end of repeat on fragment
} # Ebd of loop on file
} # End of loop on traits
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GWAS done for this Trait")
Memory=GAPIT.Memory(Memory=Memory,Infor="GWAS done for this Trait")
#print("GAPIT.EMMAxP3D accomplished successfully!")
return(list(ps = ps, REMLs = -2*REMLs, stats = stats, effect.est = effect.est, rsquare_base = rsquare_base, rsquare = rsquare, dfs = dfs, df = df, tvalue = tvalue, stderr = stderr,maf=maf,nobs = nobs,Timmer=Timmer,Memory=Memory,
vgs = vgs, ves = ves, BLUP = BLUP, BLUP_Plus_Mean = BLUP_Plus_Mean,
PEV = PEV, BLUE=BLUE, logLM = logLM,effect.snp=effect.est,effect.cv=beta.cv))
}#end of GAPIT.EMMAxP3D function
#=============================================================================================
`GAPIT.FDR.TypeI` <-
function(WS=c(1e0,1e3,1e4,1e5), GM=NULL,seqQTN=NULL,GWAS=NULL,maxOut=100,MaxBP=1e10){
#Object: To evaluate power and FDR for the top (maxOut) positive interval defined by WS
#Input: WS- window size
#Input: GM - m by 3 matrix for SNP name, chromosome and BP
#Input: seqQTN - s by 1 vecter for index of QTN on GM (+1 for GDP column wise)
#Input: GWAS - SNP,CHR,BP,P,MAF
#maxOut: maximum number of rows to report
#Requirement: None
#Output: Table and Plots
#Authors: Xiaolei Liu & Zhiwu Zhang
# Date start: April 2, 2013
# Last update: Mar 16, 2016
##############################################################################################
#print("GAPIT.Power Started")
if(is.null(seqQTN) | is.null(GM)) return(list(Power=NULL,FDR= NULL,TypeI= NULL,False= NULL,AUC.FDR= NULL,AUC.T1= NULL))
#store number fdr and t1 records
NQTN=length(seqQTN)
table=array(NA,dim=c(NQTN,2*length(WS)))
fdrtable=array(NA,dim=c(NQTN,2*length(WS)))
t1table=array(NA,dim=c(NQTN,2*length(WS)))
cutoff=array(NA,dim=c(length(WS),NQTN))
cut=array(NA,dim=c(1,NQTN))
#-----------------FDR and Power analysis-------------------------
#Information needed: GWAS,myGM and QTN(r)
GWAS=GWAS[order(GWAS[,2],GWAS[,3]),]
GWAS[is.na(GWAS[,4]),4]=1
QTN.list=sort(GWAS[seqQTN,4])
powerlist=seq(1/length(QTN.list),1,length.out=length(QTN.list))
#calculate number of false positives in each WS
total.index=1:nrow(GM)
theWS=1
for (theWS in 1:length(WS)){
wsws=WS[theWS]
qtn.pool=ceiling((as.numeric(GWAS[seqQTN,2])*MaxBP+as.numeric(GWAS[seqQTN,3]))/(2*wsws))
bonf.pool=ceiling((GWAS[total.index,2]*MaxBP+GWAS[total.index,3])/(2*wsws))
false.number=length(levels(factor(bonf.pool[!(bonf.pool%in%qtn.pool)])))
for(j in 1:length(qtn.pool)){
pbin=min(GWAS[bonf.pool==qtn.pool[j],4])
cut[,j]=pbin
}
if(theWS==1){
totalfalse=false.number
}else{
totalfalse=c(totalfalse,false.number)
}
cutoff[theWS,]=sort(cut)
}
#Calculate FDR and T1
for(j in 1:ncol(cutoff)){
theWS=1
for (theWS in 1:length(WS)){
p.index=which(GWAS[,4]<=cutoff[theWS,j])
wsws=WS[theWS]
qtn.pool=ceiling((GWAS[seqQTN,2]*MaxBP+GWAS[seqQTN,3])/(2*wsws))
bonf.pool=ceiling((GWAS[p.index,2]*MaxBP+GWAS[p.index,3])/(2*wsws))
qtn.number=length(levels(factor(bonf.pool[bonf.pool%in%qtn.pool])))
false.number=length(levels(factor(bonf.pool[!(bonf.pool%in%qtn.pool)])))
if(theWS==1){
final=false.number
final.fdr=false.number/(qtn.number+false.number)
final.t1=false.number/totalfalse[theWS]
}else{
record=false.number
record.fdr=false.number/(qtn.number+false.number)
record.t1=false.number/totalfalse[theWS]
final=c(final,record)
final.fdr=c(final.fdr,record.fdr)
final.t1=c(final.t1,record.t1)
}
}
#record FDR and T1
if(j==1){
number.record=final
fdr.record=final.fdr
t1.record=final.t1
}else{
number.record=rbind(number.record,final)
fdr.record=rbind(fdr.record,final.fdr)
t1.record=rbind(t1.record,final.t1)
}
}
table=number.record
fdrtable=fdr.record
t1table=t1.record
#AUC
auc.final.fdr=NULL
auc.final.t1=NULL
for (theWS in 1:length(WS)){
auc.fdr=GAPIT.AUC(beta=powerlist,alpha=fdrtable[,theWS])
auc.t1=GAPIT.AUC(beta=powerlist,alpha=t1table[,theWS])
auc.final.fdr=c(auc.final.fdr,auc.fdr)
auc.final.t1=c(auc.final.t1,auc.t1)
}
return(list(P=cutoff,Power=powerlist,FDR=fdrtable,TypeI=t1table,False=table,AUC.FDR=auc.final.fdr,AUC.T1=auc.final.t1))
}#end of `GAPIT.FDR.TypeI`
#=============================================================================================`GAPIT.FilterByTaxa` <-
function(taxa,Data){
#Object: To filter a data (Y, CV or GD) by taxa
#Input: taxa - vector of taxa
#Input: data - data frame with first column as taxa
#Requirement: all taxa must be in data
#Output: filtered data
#Authors: Zhiwu Zhang
# Last update: May 22, 2013
##############################################################################################
#print("GAPIT.FilterByTaxa Started")
Data=Data[match(taxa, Data[,1], nomatch = 0),]
return (Data)
}#The function GAPIT.FilterByTaxa ends here
#=============================================================================================
`GAPIT.Fragment` <-
function(file.path=NULL,file.from=NULL, file.to=NULL,file.total=NULL,file.G=NULL,
file.Ext.G=NULL,seed=123,SNP.fraction=1,SNP.effect="Add",SNP.impute="Middle",
genoFormat=NULL, file.GD=NULL, file.Ext.GD=NULL, file.GM=NULL, file.Ext.GM=NULL, file.fragment=NULL,
file=1,frag=1,LD.chromosome=NULL,LD.location=NULL,LD.range=NULL, Create.indicator = FALSE, Major.allele.zero = FALSE){
#Object: To load SNPs on a (frag)ment in file (this is to replace sampler)
#Output: genotype data sampled
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: August 18, 2011
##############################################################################################
#print("Fragmental reading...")
genoFormat="hapmap"
if(!is.null(file.GD)&is.null(file.G)) genoFormat="EMMA"
if(genoFormat=="hapmap"){
#Initical G
#print("Reading file...")
G=NULL
if(frag==1){
skip.1=0
G <- try(read.delim(paste(file.path,file.G,file, ".",file.Ext.G,sep=""),
head = FALSE,skip = skip.1, nrows = file.fragment+1),silent=TRUE)
}else{
skip.1 <- (frag-1)*file.fragment +1
G <- try(read.delim(paste(file.path,file.G,file, ".",file.Ext.G,sep=""),
head = FALSE,skip = skip.1, nrows = file.fragment),silent=TRUE )
}
#print("processing the data...")
if(inherits(G, "try-error")) {
G=NULL
#print("File end reached for G!!!")
}
if(is.null(G)){
#print("The above error indicating reading after end of file (It is OK).")
return(list(GD=NULL,GI=NULL,GT=NULL,linesRead=NULL,GLD=NULL,heading=NULL) )
}
#print("Calling hapmap...")
heading=(frag==1)
#Recording number of lineas read
if(heading){
n= nrow(G)-1
}else{
n= nrow(G)
}
linesRead=n
#Sampling
if(SNP.fraction<1){
#print("Number of SNP in this pragment:")
#print(n)
#set.seed(seed+(file*1000)+frag)
#mySample=sample(1:n,max(2,floor(n*as.numeric(as.vector(SNP.fraction)))))
mySample=sample(1:n,max(2,floor(n*SNP.fraction)))
#print("@@@@@@@@@@")
#print(mySample)
#print(length(mySample))
if(heading){
G=G[c(1,(1+mySample)),]
}else{
G=G[mySample,]
}
} #end of if(SNP.fraction<1)
print("Call hapmap from fragment")
hm=GAPIT.HapMap(G,SNP.effect=SNP.effect,SNP.impute=SNP.impute,heading=heading, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
#print("Extracting snps for LD plot...")
#Extract SNPs for LD plot
if(!is.null(LD.chromosome) & !is.null(hm$GD)){
index=(G[,3]==LD.chromosome[1]) & abs((as.numeric(G[,4])-as.numeric(LD.location[1]))<(as.numeric(LD.range[1])/2))
GLD=G[index,]
}else{
GLD=NULL
}
#rm(G)
#gc()
print("hapmap called successfuly from fragment")
return(list(GD=hm$GD,GI=hm$GI,GT=hm$GT,linesRead=linesRead,GLD=GLD,heading=heading,G=G))
print("ERROR: It should not get here!!!")
} #end of "hapmap"
if(genoFormat=="EMMA"){
#print("The file is a numerical format!")
#Initial GD
GD=NULL
skip.1 <- (frag-1)*file.fragment
#Skip the remaining columns
GD.temp <- try(read.table(paste(file.path,file.GD, file, ".", file.Ext.GD,sep=""), head = TRUE, nrows = 1),silent=TRUE)
num.SNP <- ncol(GD.temp)-1
rm(GD.temp)
read.in <- min(file.fragment,(num.SNP-skip.1))
skip.2 <- max((num.SNP - (skip.1 + read.in)),0)
print(paste(file.path,file.GD,file, ".",file.Ext.GD,sep=""))
GD <- try(read.table(paste(file.path,file.GD,file, ".",file.Ext.GD,sep=""), head = TRUE,
colClasses = c("factor", rep("NULL", skip.1), rep("numeric", read.in),
rep("NULL", skip.2))) ,silent=TRUE)
GI <- try(read.table(paste(file.path,file.GM,file, ".",file.Ext.GM,sep=""), head = TRUE,
skip=skip.1, nrows=file.fragment) ,silent=TRUE)
if(inherits(GD, "try-error")) {
GD=NULL
print("File end reached for GD!!!")
}
if(inherits(GI, "try-error")) {
GI=NULL
print("File end reached for GI!!!")
}
if(is.null(GD)) return(list(GD=NULL, GI=NULL,GT=NULL,linesRead=NULL,GLD=NULL))
GT=GD[,1] #Extract infividual names
GD=GD[,-1] #Remove individual names
#print("Numerical file read sucesfuly from fragment")
linesRead=ncol(GD)
if(SNP.fraction==1) return(list(GD=GD, GI=GI,GT=GT,linesRead=linesRead,GLD=NULL))
if(SNP.fraction<1){
n= ncol(GD)
#set.seed(seed+file)
sample=sample(1:n,floor(n*SNP.fraction))
return(list(GD=GD[,sample], GI=GI[sample,],GT=GT,linesRead=linesRead,GLD=NULL))
}
} # end of the "EMMA"
#print("fragment ended succesfully!")
}#End of fragment
#=============================================================================================
`GAPIT.GS` <-
function(KW,KO,KWO,GAU,UW){
#Object: to derive BLUP for the individuals without phenotype
#UW:BLUP and PEV of ID with phenotyp
#Output: BLUP
#Authors: Zhiwu Zhang
# Last update: Oct 22, 2015 by Jiabo Wang
##############################################################################################
#print(dim(UW))
UO=try(t(KWO)%*%solve(KW)%*%UW,silent=TRUE)
#print(dim(KWO)) #kinship without inference
#print(dim(KW)) #kinship within inference
#print(dim(UW)) #BLUP AND PEV of reference
if(inherits(UO, "try-error")) UO=t(KWO)%*%ginv(KW)%*%UW
n=ncol(UW) #get number of columns, add additional for individual name
BLUP=data.frame(as.matrix(GAU[,1:4]))
BLUP.W=BLUP[which(GAU[,3]<2),]
W_BLUP=BLUP.W[order(as.numeric(as.matrix(BLUP.W[,4]))),]
UW=UW[which(rownames(UW)==colnames(KW)),] # get phenotype groups order
ID.W=as.numeric(as.matrix(W_BLUP[,4]))
n.W=max(ID.W)
DS.W=diag(n.W)[ID.W,]
ind.W=DS.W%*%UW
all.W=cbind(W_BLUP,ind.W)
all=all.W
BLUP.O=BLUP[which(GAU[,3]==2),]
O_BLUP=BLUP.O[order(as.numeric(as.matrix(BLUP.O[,4]))),]
#print(dim(O_BLUP))
if(nrow(O_BLUP)>0){
ID.O=as.numeric(as.matrix(O_BLUP[,4]))
n.O=max(ID.O)
DS.O=diag(n.O)[ID.O,]
ind.O=DS.O%*%UO
all.O=cbind(O_BLUP,ind.O)
all=rbind(all.W,all.O)
}
colnames(all)=c("Taxa", "Group", "RefInf","ID","BLUP","PEV")
print("GAPIT.GS accomplished successfully!")
return(list(BLUP=all))
}#The function GAPIT.GS ends here
#=============================================================================================
`GAPIT.GS.Visualization` <-
function(gsBLUP = gsBLUP, BINS=BINS, name.of.trait = name.of.trait){
#Object: To build heat map to show distribution of BLUP and PEV
#Output: pdf
#Authors: Zhiwu Zhang
# Last update: May 15, 2011
##############################################################################################
nBin=BINS
BLUP= gsBLUP[,5]
PEV = gsBLUP[,6]
if(BLUP[1]=="NaN"){
warning ("It was not converged. BLUP was not created!")
}
if(BLUP[1]!="NaN" )
{
BLUP.max=try(max(BLUP))
BLUP.min=try(min(BLUP))
if(inherits(BLUP.max, "try-error")) return()
range.BLUP=BLUP.max-BLUP.min
range.PEV=max(PEV)-min(PEV)
interval.BLUP=range.BLUP/nBin
interval.PEV=range.PEV/nBin
bin.BLUP=floor(BLUP/max(BLUP)*nBin)*max(BLUP)/nBin
bin.PEV=floor(PEV/max(PEV)*nBin)*max(PEV)/nBin
distinct.BLUP=unique(bin.BLUP)
distinct.PEV=unique(bin.PEV)
if((length(distinct.BLUP)<2) | (length(distinct.PEV)<2) ) return() #nothing to plot
Position.BLUP=match(bin.BLUP,distinct.BLUP,nomatch = 0)
Position.PEV=match(bin.PEV,distinct.PEV,nomatch = 0)
value=matrix(1,length(Position.BLUP))
KG<- (tapply(as.numeric(value), list(Position.BLUP, Position.PEV), sum))
rownames(KG)=round(distinct.BLUP, digits = 4)
colnames(KG)=round(distinct.PEV, digits = 4)
#Sort the rows and columns in order from smallest to largest
rownames(KG) <- rownames(KG)[order(as.numeric(rownames(KG)))]
colnames(KG) <- colnames(KG)[order(as.numeric(colnames(KG)))]
rownames(KG) <- round(as.numeric(rownames(KG)))
colnames(KG) <- round(as.numeric(colnames(KG)))
#write.table(KG, "Input_Matrix_for_GS_Heat_Map.txt", quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
pdf(paste("GAPIT.", name.of.trait,".GPS.BLUPvsPEV", ".pdf", sep = ""),width = 9)
#par(mfrow = c(1,1), mar = c(1,1,5,5), lab = c(5,5,7))
par(mar = c(5,5,6,5))
nba_heatmap <- heatmap.2(KG, Rowv=NA, Colv=NA, col = rev(heat.colors(256)), # scale="column",
xlab = "PEV", ylab = "BLUP", main = " ", scale="none", symkey=FALSE, trace="none")
#nba_heatmap <- heatmap.2(KG, cexRow =.2, cexCol = 0.2, scale="none", symkey=FALSE, trace="none" )
#cexRow =0.9, cexCol = 0.9)
dev.off()
}
#print("GAPIT.GS.Visualization accomplished successfully!")
} #GAPIT.GS.Visualization ends here
#=============================================================================================
`GAPIT.Genotype` <-
function(G=NULL,GD=NULL,GM=NULL,KI=NULL,
kinship.algorithm="Zhang",SNP.effect="Add",SNP.impute="Middle",PCA.total=0,PCA.col=NULL,PCA.3d=PCA.3d,seed=123, SNP.fraction =1,
file.path=NULL,file.from=NULL, file.to=NULL, file.total=NULL, file.fragment = 1000,SNP.test=TRUE,
file.G =NULL,file.Ext.G =NULL,
file.GD=NULL,file.Ext.GD=NULL,
file.GM=NULL,file.Ext.GM=NULL,
SNP.MAF=0.05,FDR.Rate = 0.05,SNP.FDR=1,
Timmer=NULL,Memory=NULL,
LD.chromosome=NULL,LD.location=NULL,LD.range=NULL, SNP.CV=NULL,
GP = NULL,GK = NULL,GTindex=NULL,
bin.size = 1000,inclosure.size = 100,
sangwich.top=NULL,sangwich.bottom=NULL,
file.output=TRUE,kinship.cluster="average",NJtree.group=NULL,NJtree.type=c("fan","unrooted"),
Create.indicator = FALSE, Major.allele.zero = FALSE,Geno.View.output=TRUE){
#Object: To unify genotype and calculate kinship and PC if required:
# 1.For G data, convert it to GD and GI
# 2.For GD and GM data, nothing change
# 3.Samling GD and create KI and PC
# 4.Go through multiple files
# 5.In any case, GD must be returned (for QC)
#Output: GD, GI, GT, KI and PC
#Authors: Zhiwu Zhang
#Last update: August 11, 2011
##############################################################################################
#print("Genotyping: numericalization, sampling kinship, PCs and much more...")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype start")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype start")
#Create logical variables
byData=!is.null(G) | !is.null(GD)
byFile=!is.null(file.G) | !is.null(file.GD)
hasGenotype=(byData | byFile )
needKinPC=(is.null(KI) | PCA.total>0 | kinship.algorithm=="Separation")
if(!is.null(KI) & !byData & !byFile & !SNP.test &kinship.algorithm!="SUPER") {
print("It return unexpected")
return (list(GD=NULL,GI=NULL,GT=NULL,hasGenotype=FALSE, genoFormat=NULL, KI=KI,PC=NULL,byFile=FALSE,fullGD=TRUE,Timmer=Timmer,Memory=Memory))
}
#Set indicator for full GD
fullGD=FALSE
if(byData) fullGD=TRUE
if(byFile & SNP.fraction==1 & needKinPC) fullGD=TRUE
#SET GT to NULL in case of no genotype
if(!byData & !byFile & is.null(GK) &kinship.algorithm!="SUPER") {
if(is.null(KI) & is.null(GP) & is.null(GK)) stop("GAPIT says: Kinship has to be provided or estimated from genotype!!!")
return (list(GD=NULL,GI=NULL,GT=NULL,hasGenotype=FALSE, genoFormat=NULL, KI=KI,PC=NULL,byFile=FALSE,fullGD=TRUE,Timmer=Timmer,Memory=Memory))
}
genoFormat="hapmap"
if(is.null(G)&is.null(file.G)) genoFormat="EMMA"
#Multiple genotype files
#In one of the 3 situations, calculate KI with the algorithm specified, otherwise skip cit by setting algorithm to "SUPER"
kinship.algorithm.save=kinship.algorithm
kinship.algorithm="SUPER"
#Normal
if(is.null(sangwich.top) & is.null(sangwich.bottom) ) kinship.algorithm=kinship.algorithm.save
#TOP or Bottom is MLM
pass.top=FALSE
if(!is.null(sangwich.top)) pass.top=!(sangwich.top=="FaST" | sangwich.top=="SUPER" | sangwich.top=="DC")
pass.bottom=FALSE
if(!is.null(sangwich.bottom)) pass.bottom=!(sangwich.bottom=="FaST" | sangwich.bottom=="SUPER" | sangwich.bottom=="DC")
if(pass.top | pass.bottom )kinship.algorithm=kinship.algorithm.save
#Compatibility of input
#agreement among file from, to and total
if(!is.null(file.from) &!is.null(file.to) &!is.null(file.total)){
if(file.total!=(file.to-file.from+1)) stop("GAPIT says: Conflict among file (from, to and total)")
}
if(!is.null(file.from) &!is.null(file.to)) {
if(file.to<file.from) stop("GAPIT says: file.from should smaller than file.to")
}
#file.from and file.to must be in pair
if(is.null(file.from) &!is.null(file.to) ) stop("GAPIT says: file.from and file.to must be in pair)")
if(!is.null(file.from) &is.null(file.to) ) stop("GAPIT says: file.from and file.to must be in pair)")
#assign file.total
if(!is.null(file.from) &!is.null(file.to) ) file.total=file.to-file.from+1
if(byFile& is.null(file.total)) stop("GAPIT says: file.from and file.to must be provided!)")
if(!is.null(GP) & !is.null(GK) ) stop("GAPIT Says: You can not provide GP and GK at same time")
if(!is.null(GP) & !is.null(KI) ) stop("GAPIT Says: You can not provide GP and KI at same time")
if(!is.null(GK) & !is.null(KI)) stop("GAPIT says: You can not specify GK and KI at same time!!!")
#GP does not allow TOP
if(!is.null(GP) & !is.null(sangwich.top) ) stop("GAPIT Says: You provided GP. You can not spycify sangwich.top")
#Top require a bottom
if(!is.null(sangwich.top) & is.null(sangwich.bottom) ) stop("GAPIT Says: Top require its Bottom")
#naked bottom require GP or GK
if(is.null(sangwich.top) & !is.null(sangwich.bottom) & (is.null(GP) & is.null(GK)) ) stop("GAPIT Says: Uncovered Bottom (without TOP) requires GP or GK")
#Pseudo top (GK or GP) requires a bottom
if(is.null(sangwich.top) & is.null(sangwich.bottom) & (!is.null(GP)|!is.null(GK ))) stop("GAPIT Says: You have provide GP or GK, you need to provide Bottom")
#if(!is.null(KI) &!is.null(kinship.algorithm)) stop("GAPIT says: You can not specify kinship.algorithm and provide kinship at same time!!!")
if(!needKinPC &SNP.fraction<1) stop("GAPIT says: You did not require calculate kinship or PCs. SNP.fraction should not be specified!!!")
if(!SNP.test & is.null(KI) & !byData & !byFile) stop("GAPIT says: For SNP.test optioin, please input either use KI or use genotype")
#if(is.null(file.path) & !byData & byFile) stop("GAPIT Ssays: A path for genotype data should be provided!")
if(is.null(file.total) & !byData & byFile) stop("GAPIT Ssays: Number of file should be provided: >=1")
if(!is.null(G) & !is.null(GD)) stop("GAPIT Ssays: Both hapmap and EMMA format exist, choose one only.")
if(!is.null(file.GD) & is.null(file.GM) & (!is.null(GP)|!is.null(GK)) ) stop("GAPIT Ssays: Genotype data and map files should be in pair")
if(is.null(file.GD) & !is.null(file.GM) & (!is.null(GP)|!is.null(GK)) ) stop("GAPIT Ssays: Genotype data and map files should be in pair")
if(!is.null(GD) & is.null(GM) & (is.null(GP)&is.null(GK)) &kinship.algorithm!="SUPER") stop("GAPIT Says: Genotype data and map files should be in pair")
if(is.null(GD) & !is.null(GM) & (is.null(GP)&is.null(GK)) &kinship.algorithm!="SUPER") stop("GAPIT Says: Genotype data and map files should be in pair")
#if(!byData & !byFile) stop("APIT Ssays: Either genotype data or files should be given!")
#if(byData&(!is.null(file.path))) stop ("APIT Ssays: You have provided geotype data. file.path should not be provided!")
#print("Pass compatibility of input")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype loaded")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype loaded")
#Inital GLD
GLD=NULL
SNP.QTN=NULL #Intitial
GT=NULL
#Handler of read data in numeric format (EMMA)
#Rename GM as GI
if(!is.null(GM))GI=GM
rm(GM)
gc()
#Extract GD and GT from read data GD
if(!is.null(GD) )
{
GT=as.matrix(GD[,1]) #get taxa
GD=as.matrix(GD[,-1]) #remove taxa column
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GT created from GD)")
Memory=GAPIT.Memory(Memory=Memory,Infor="GT created from GD")
}
#Hapmap format
if(!is.null(G))
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before HapMap")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before HapMap")
#Convert HapMap to numerical
print(paste("Converting genotype...",sep=""))
hm=GAPIT.HapMap(G,SNP.effect=SNP.effect,SNP.impute=SNP.impute, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="after HapMap")
Memory=GAPIT.Memory(Memory=Memory,Infor="after HapMap")
#Extracting SNP for LD plot
if(!is.null(LD.chromosome)){
#print("Extracting SNP for LD plot...")
chromosome=(G[,3]==LD.chromosome[1])
bp=as.numeric(as.vector(G[,4]))
deviation=abs(bp-as.numeric(as.vector(LD.location[1])) )
location=deviation< as.numeric(as.vector(LD.range[1]) )
index=chromosome&location
GLD=G[index,]
}else{
#print("No data in GLD")
GLD=NULL
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="HapMap")
Memory=GAPIT.Memory(Memory=Memory,Infor="HapMap")
print(paste("Converting genotype done.",sep=""))
#rm(G)
#gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="G removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="G removed")
GT=hm$GT
GD=hm$GD
GI=hm$GI
#print(unique(GI[,2]))
rm(hm)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="hm removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="hm removed")
}
#From files
if(!byData & byFile){
#print("Loading genotype from files...")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="byFile")
Memory=GAPIT.Memory(Memory=Memory,Infor="byFile")
numFileUsed=file.to
if(!needKinPC)numFileUsed=file.from
#Initial GI as storage
GD=NULL
GT=NULL
GI=NULL
GLD=NULL
#multiple fragments or files
for (file in file.from:numFileUsed){
frag=1
numSNP=file.fragment
myFRG=NULL
#print(paste("numSNP before while is ",numSNP))
while(numSNP==file.fragment) { #this is problematic if the read end at the last line
print(paste("Reading file: ",file,"Fragment: ",frag))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before Fragment")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before Fragment")
myFRG=GAPIT.Fragment( file.path=file.path,file.from=file.from, file.to=file.to,file.total=file.total,file.G=file.G,file.Ext.G=file.Ext.G,
seed=seed,SNP.fraction=SNP.fraction,SNP.effect=SNP.effect,SNP.impute=SNP.impute,genoFormat=genoFormat,
file.GD=file.GD,file.Ext.GD=file.Ext.GD,file.GM=file.GM,file.Ext.GM=file.Ext.GM,
file.fragment=file.fragment,file=file,frag=frag,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
#print(paste("numSNP after while is ",numSNP))
#print(paste("OK with file: ",file,"Fragment: ",frag))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="After Fragment")
Memory=GAPIT.Memory(Memory=Memory,Infor="After Fragment")
if(is.null(GT) & !is.null(myFRG$GT))GT= as.matrix(myFRG$GT)
if(is.null(GD)){
GD= myFRG$GD
}else{
if(!is.null(myFRG$GD)) {
GD=cbind(GD,myFRG$GD)
}
}
if(is.null(GI)){
GI= myFRG$GI
}else{
if(!is.null(myFRG$GI)) {
colnames(myFRG$GI)=c("SNP","Chromosome","Position")
GI=as.data.frame(rbind(as.matrix(GI),as.matrix(myFRG$GI)))
}
}
if(is.null(G)){
G= myFRG$G
}else{
if(!is.null(myFRG$G)) {
G=as.data.frame(rbind(as.matrix(G),as.matrix(myFRG$G[-1,])))
}
}
if(is.null(GLD)){
GLD= myFRG$GLD
}else{
if(!is.null(myFRG$GLD)) {
if(myFRG$heading){
GLD=as.data.frame(rbind(as.matrix(GLD),as.matrix(myFRG$GLD[-1,])))
}else{
GLD=as.data.frame(rbind(as.matrix(GLD),as.matrix(myFRG$GLD)))
}
}
}
#print("This fragment is joined")
if(file==file.from & frag==1)GT=as.matrix(myFRG$GT)
frag=frag+1
if(!is.null(myFRG$GI)) {
numSNP=myFRG$linesRead[1]
}else{
numSNP=0
}
if(!needKinPC)numSNP=0 #force to end the while loop
if(is.null(myFRG))numSNP=0 #force to end the while loop
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="END this Fragment")
Memory=GAPIT.Memory(Memory=Memory,Infor="END this Fragment")
} #end of repeat on fragment
# print("This file is OK")
} #end of file loop
print("All files loaded")
} #end of if(!byData&byFile)
#GM=as.matrix(GI)
#GI=GM
GM=GI
#print(unique(GM[,2]))
#print("@@@@@@@@@@")
#Set the number of chromosome
# if(1%in%as.character(unique(GM[,2])))
# { chor_taxa=mixedsort(as.character((unique(GM[,2]))))
# }else{
# chor_taxa=as.character(unique(GM[,2]))
# #print(chor_taxa)
# for(i in 1:(length(chor_taxa)))
# {
# index=GM[,2]==chor_taxa[i]
# GI[index,2]=i
# }
# }
# modified by Jiabo in 20190927. sorted number of chrom by numeric and charicter
chor_taxa=as.character(unique(GM[,2]))
chor_taxa[order(gsub("([A-Z]+)([0-9]+)", "\\1", chor_taxa),
as.numeric(gsub("([A-Z]+)([0-9]+)", "\\2", chor_taxa)))]
chr_letter=grep("[A-Z]|[a-z]",chor_taxa)
if(!setequal(integer(0),chr_letter))
{
GI=as.matrix(GI)
for(i in 1:(length(chor_taxa)))
{
index=GM[,2]==chor_taxa[i]
GI[index,2]=i
}
}
#print(head(GI))
#print(head(GI))
#print("@@@@@@@@@@@")
#print(GD[1:5,1:5])
#print(dim(GI))
#Follow the MAF to filter markers
if(!is.null(GD))
{
#maf=apply(as.matrix(GD),2,function(one) abs(1-sum(one)/(2*nrow(GD))))
#maf[maf>0.5]=1-maf[maf>0.5]
ss=apply(GD,2,sum)
maf=apply(cbind(.5*ss/(nrow(GD)),1-.5*ss/(nrow(GD))),1,min)
#print(max(maf))
#print(min(maf))
maf_index=maf>=SNP.MAF
print(paste("GAPIT will filter marker with MAF setting !!"))
print(paste("The markers will be filtered by SNP.MAF: ",SNP.MAF,sep=""))
print(table(maf_index))
#print(head(maf[!maf_index]))
GD=GD[,maf_index]
GM=as.data.frame(GI[maf_index,])
GI=GM
}
#print("file loaded")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Sampling genotype")
Memory=GAPIT.Memory(Memory=Memory,Infor="Sampling genotype")
#print(KI)
#Plot thirt part kinship
if(!is.null(KI) &file.output) {
if(KI!=1) {
if(nrow(KI)<1000){
print("Plotting Kinship")
#print(dim(KI))
theKin=as.matrix(KI[,-1])
line.names <- KI[,1]
colnames(theKin)=KI[,1]
rownames(theKin)=KI[,1]
distance.matrix=dist(theKin,upper=TRUE)
hc=hclust(distance.matrix,method=kinship.cluster)
hcd = as.dendrogram(hc)
##plot NJtree
if (!is.null(NJtree.group))
{
clusMember <- cutree(hc, k = NJtree.group)
compress_z=table(clusMember,paste(line.names))
type_col=rainbow(NJtree.group)
#type_col=rainbow(NJtree.group)
Optimum=c(nrow(theKin),kinship.cluster,NJtree.group)
#rm(distance.matrix,hc)
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="set kinship")
Memory=GAPIT.Memory(Memory=Memory,Infor="set kinship")
print("Creating heat map for kinship...")
pdf(paste("GAPIT.Kin.thirdPart.pdf",sep=""), width = 12, height = 12)
par(mar = c(25,25,25,25))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="prepare heatmap")
Memory=GAPIT.Memory(Memory=Memory,Infor="prepare heatmap")
heatmap.2(theKin, cexRow =.2, cexCol = 0.2, col=rev(heat.colors(256)), scale="none", symkey=FALSE, trace="none")
dev.off()
print("Kinship heat map PDF created!")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="plot heatmap")
Memory=GAPIT.Memory(Memory=Memory,Infor="plot heatmap")
## Jiabo Wang add NJ Tree of kinship at 4.5.2017
if (!is.null(NJtree.group))
{
for(tr in 1:length(NJtree.type))
{
print("Creating NJ Tree for kinship...")
pdf(paste("GAPIT.Kin.NJtree.",NJtree.type[tr],".pdf",sep=""), width = 12, height = 12)
par(mar = c(5,5,5,5))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="prepare NJ TREE")
Memory=GAPIT.Memory(Memory=Memory,Infor="prepare NJ TREE")
plot(as.phylo(hc), type = NJtree.type[tr], tip.color =type_col[clusMember], use.edge.length = TRUE, col = "gray80",cex=0.6)
#legend("topright",legend=c(paste("Tatal numerber of individuals is ",),lty=0,cex=1.3,bty="n",bg=par("bg"))
legend("topright",legend=paste(c("Tatal individuals is: ","Cluster method: ","Group number: "), Optimum[c(1:3)], sep=""),lty=0,cex=1.3,bty="n",bg=par("bg"))
dev.off()
}
write.table(compress_z,paste("GAPIT.Kin.NJtree.compress_z.txt",sep=""),quote=F)
print("Kinship NJ TREE PDF created!")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="plot NJ TREE")
Memory=GAPIT.Memory(Memory=Memory,Infor="plot NJ TREE")
#rm(hc,clusMember)
}#end
## NJ Tree end
} #end of if(nrow(KI)<1000)
} #end of if(KI!=1)
} #end of if(!is.null(KI))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before SUPER")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before SUPER")
#SUPER
if(!is.null(GP) & kinship.algorithm=="SUPER" & !is.null(bin.size) & !is.null(inclosure.size)){
mySpecify=GAPIT.Specify(GI=GI,GP=GP,bin.size=bin.size,inclosure.size=inclosure.size)
SNP.QTN=mySpecify$index
if(!is.null(GD)){
#comment out to keep all taxa for GS, Zhiwu (Dec7, 2012)
#GK=GD[GTindex,SNP.QTN]
#SNPVar=apply(as.matrix(GK),2,var)
#GK=GK[,SNPVar>0]
#GK=cbind(as.data.frame(GT[GTindex]),as.data.frame(GK)) #add taxa
GK=GD[,SNP.QTN]
SNPVar=apply(as.matrix(GK),2,var)
GK=GK[,SNPVar>0]
GK=cbind(as.data.frame(GT),as.data.frame(GK)) #add taxa
#print("QTN extracted")
}
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before creating kinship")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before creating kinship")
#Create kinship from genotype if not provide
if(is.null(KI) & (!is.null(GD) |!is.null(GK)) & !kinship.algorithm%in%c("FarmCPU","Blink","MLMM"))
{
print("Calculating kinship...")
if(!is.null(GK)){
thisGD=GK[,-1]
myGT=as.matrix(GK[,1])
print("GK is used to create KI")
}else{
thisGD=GD
myGT=GT
#comment out to keep all taxa for GS, Zhiwu (Dec7, 2012)
#if(!is.null(GTindex)){
# thisGD=thisGD[GTindex,]
# myGT=myGT[GTindex]
#}
}
print(paste("Number of individuals and SNPs are ",nrow(thisGD)," and ",ncol(thisGD)))
theKin=NULL
if(kinship.algorithm=="EMMA"){
half.thisGD = as.matrix(.5*thisGD)
if(length(which(is.na(half.thisGD))) > 0){
print("Substituting missing values with heterozygote for kinship matrrix calculation....")
half.thisGD[which(is.na(half.thisGD))] = 1
}
theKin= emma.kinship(snps=t(as.matrix(.5*thisGD)), method="additive", use="all")
}
if(kinship.algorithm=="Loiselle")theKin= GAPIT.kinship.loiselle(snps=t(as.matrix(.5*thisGD)), method="additive", use="all")
if(kinship.algorithm=="VanRaden")theKin= GAPIT.kinship.VanRaden(snps=as.matrix(thisGD))
if(kinship.algorithm=="Zhang")theKin= GAPIT.kinship.ZHANG(snps=as.matrix(thisGD))
if(kinship.algorithm=="Separation")theKin= GAPIT.kinship.separation(PCs=thePCA$PCs,EV=thePCA$EV,nPCs=PCA.total)
if(!is.null(theKin)){
colnames(theKin)=myGT
rownames(theKin)=myGT
line.names <- myGT
if (!is.null(NJtree.group))
{
distance.matrix=dist(theKin,upper=TRUE)
hc=hclust(distance.matrix,method=kinship.cluster)
hcd = as.dendrogram(hc)
clusMember <- cutree(hc, k = NJtree.group)
compress_z=table(clusMember,paste(line.names))
type_col=rainbow(NJtree.group)
Optimum=c(nrow(theKin),kinship.cluster,NJtree.group)
}
#print(Optimum)
print("kinship calculated")
if(length(GT)<1000 &file.output){
#Create heat map for kinship
print("Creating heat map for kinship...")
pdf(paste("GAPIT.Kin.",kinship.algorithm,".pdf",sep=""), width = 12, height = 12)
par(mar = c(25,25,25,25))
heatmap.2(theKin, cexRow =.2, cexCol = 0.2, col=rev(heat.colors(256)), scale="none", symkey=FALSE, trace="none")
dev.off()
print("Kinship heat map created")
## Jiabo Wang add NJ Tree of kinship at 4.5.2017
if (!is.null(NJtree.group))
{
print("Creating NJ Tree for kinship...")
for(tr in 1:length(NJtree.type))
{
pdf(paste("GAPIT.Kin.NJtree.",NJtree.type[tr],".pdf",sep=""), width = 12, height = 12)
par(mar = c(0,0,0,0))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="prepare NJ TREE")
Memory=GAPIT.Memory(Memory=Memory,Infor="prepare NJ TREE")
plot(as.phylo(hc), type = NJtree.type[tr], tip.color =type_col[clusMember], use.edge.length = TRUE, col = "gray80",cex=0.6)
#legend("topright",legend=c(paste("Tatal numerber of individuals is ",),lty=0,cex=1.3,bty="n",bg=par("bg"))
legend("topright",legend=paste(c("Tatal individuals is: ","Group method: ","Group number: "), Optimum[c(1:3)], sep=""),lty=0,cex=1.3,bty="n",bg=par("bg"))
dev.off()
}
# print(Optimum)
write.table(compress_z,paste("GAPIT.Kin.NJtree.compress_z.txt",sep=""),quote=F)
print("Kinship NJ TREE PDF created!")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="plot NJ TREE")
Memory=GAPIT.Memory(Memory=Memory,Infor="plot NJ TREE")
rm(hc)
}#end NJtree
}
print("Adding IDs to kinship...")
#Write the kinship into a text file
KI=cbind(myGT,as.data.frame(theKin)) #This require big memory. Need a way to solve it.
print("Writing kinship to file...")
if(file.output) write.table(KI, paste("GAPIT.Kin.",kinship.algorithm,".csv",sep=""), quote = FALSE, sep = ",", row.names = FALSE,col.names = FALSE)
print("Kinship save as file")
rm(theKin)
gc()
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Estimating kinship")
Memory=GAPIT.Memory(Memory=Memory,Infor="Estimating kinship")
print("Kinship created!")
} #end of if(is.null(KI)&!is.null(GD))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="after creating kinship")
Memory=GAPIT.Memory(Memory=Memory,Infor="after creating kinship")
#LD plot
#print("LD section")
if(!is.null(GLD) &file.output){
if(nrow(GLD)>500){
GLD=GLD[1,]
print("WARNING: The number of SNPs requested is beyond limitation. No LD plot created.")
}
if(nrow(GLD)>1)
{
print("Plot LD...")
hapmapgeno= data.frame(as.matrix(t(GLD[,-c(1:11)])))
hapmapgeno[hapmapgeno=="NN"]=NA
hapmapgeno[hapmapgeno=="XX"]=NA
hapmapgeno[hapmapgeno=="--"]=NA
hapmapgeno[hapmapgeno=="++"]=NA
hapmapgeno[hapmapgeno=="//"]=NA
LDdist=as.numeric(as.vector(GLD[,4]))
LDsnpName=GLD[,1]
colnames(hapmapgeno)=LDsnpName
#Prune SNM names
#LDsnpName=LDsnpName[GAPIT.Pruning(LDdist,DPP=7)]
LDsnpName=LDsnpName[c(1,length(LDsnpName))] #keep the first and last snp names only
#print(hapmapgeno)
print("Getting genotype object")
LDsnp=makeGenotypes(hapmapgeno,sep="",method=as.genotype) #This need to be converted to genotype object
print("Caling LDheatmap...")
pdf(paste("GAPIT.LD.chromosom",LD.chromosome,"(",round(max(0,LD.location-LD.range)/1000000),"_",round((LD.location+LD.range)/1000000),"Mb)",".pdf",sep=""), width = 12, height = 12)
#pdf(paste("GAPIT.LD.pdf",sep=""), width = 12, height = 12)
par(mar = c(25,25,25,25))
MyHeatmap <- try(LDheatmap(LDsnp, LDdist, LDmeasure="r", add.map=TRUE,
SNP.name=LDsnpName,color=rev(cm.colors(20)), name="myLDgrob", add.key=TRUE,geneMapLabelY=0.1) )
if(!inherits(MyHeatmap, "try-error")) {
#Modify the plot
grid.edit(gPath("myLDgrob", "Key", "title"), gp=gpar(cex=.5, col="blue")) #edit key title size and color
grid.edit(gPath("myLDgrob", "geneMap", "title"), gp=gpar(just=c("center","bottom"), cex=0.8, col="black")) #Edit gene map title
grid.edit(gPath("myLDgrob", "geneMap","SNPnames"), gp = gpar(cex=0.3,col="black")) #Edit SNP name
}else{
print("Warning: error in converting genotype. No LD plot!")
}
dev.off()
print("LD heatmap crated")
#grid.edit(gPath("myLDgrob", "heatMap","title"), gp=gpar(cex=1.0)) #Make title smaler
#grid.edit(gPath("myLDgrob", "geneMap", "title"), gp=gpar(just=c("right","bottom"), cex=0.5, col="blue")) #Edit gene map title
#grid.edit(gPath("myLDgrob", "Key", "labels"), gp=gpar(cex=.5, col="black")) #edit key lable size and color
}else{ # alternative of if(nrow(GLD)>1)
print("Warning: There are less than two SNPs on the region you sepcified. No LD plot!")
} #end of #if(nrow(GLD)>1)
}#end of if(!is.null(GLD))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="after LD plot")
Memory=GAPIT.Memory(Memory=Memory,Infor="after LD plot")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before PCA")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before PCA")
#Create PC
#print(PCA.total)
PC=NULL
thePCA=NULL
if(is.null(PCA.col)&!is.null(NJtree.group))PCA.col=type_col[clusMember]
#print("!!!!!!!!!!")
#print(PCA.col)
if(PCA.total>0 | kinship.algorithm=="Separation"){
thePCA=GAPIT.PCA(X = GD, taxa = GT, PC.number = PCA.total,file.output=file.output,PCA.total=PCA.total,PCA.col=PCA.col,PCA.3d=PCA.3d)
PC=thePCA$PCs[,1:(1+PCA.total)]
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PCA")
Memory=GAPIT.Memory(Memory=Memory,Infor="PCA")
print("PC created")
}
###output Marker density and decade of linkage disequilibrium over distance
if(!is.null(GI) & !is.null(GD) & file.output & Geno.View.output){
ViewGenotype<-GAPIT.Genotype.View(
myGI=GI,
myGD=GD,
#chr=1,
#w1_start=30,
#w1_end=230,
#mav1=10
)
}
#print("Genotype successfully acomplished")
return (list(G=G,GD=GD,GI=GI,GT=GT,hasGenotype=hasGenotype, genoFormat=genoFormat, KI=KI,PC=PC,byFile=byFile,fullGD=fullGD,Timmer=Timmer,Memory=Memory,SNP.QTN=SNP.QTN,chor_taxa=chor_taxa))
}
#=============================================================================================
`GAPIT.Genotype.View` <-function(myGI=NULL,myGD=NULL,chr=NULL, w1_start=NULL,w1_end=NULL,mav1=NULL){
# Object: Analysis for Genotype data:Distribution of SNP density,Accumulation,Moving Average of density,result:a pdf of the scree plot
# myG:Genotype data
# chr: chromosome value
# w1_start:Moving Average windows Start Position
# w1_end:Moving Average windows End Position
# mav1:Moving Average set value length
# Authors: You Tang and Zhiwu Zhang
# Last update: March 11, 2016
##############################################################################################
#if(nrow(myGI)<1000) return() #Markers are not enough for this analysis
if(is.null(myGI)){stop("Validation Invalid. Please select read valid Genotype flies !")}
if(is.null(myGD)){stop("Validation Invalid. Please select read valid Genotype flies !")}
if(is.null(w1_start)){w1_start=1}
##if(is.null(w1_end)){w1_end=100}
if(is.null(mav1)){mav1=10}
if(is.null(chr)){chr=1}
#heterozygosity of individuals and SNPs (By Zhiwu Zhang)
#print("Heterozygosity of individuals and SNPs (By Zhiwu Zhang)")
X=myGD[,-1]
H=1-abs(X-1)
het.ind=apply(H,1,mean)
het.snp=apply(H,2,mean)
ylab.ind=paste("Frequency (out of ",length(het.ind)," individuals)",sep="")
ylab.snp=paste("Frequency (out of ",length(het.snp)," markers)",sep="")
pdf("GAPIT.Heterozygosity.pdf", width =10, height = 6)
par(mfrow=c(1,2),mar=c(5,5,1,1)+0.1)
hist(het.ind,col="gray", main="",ylab=ylab.ind, xlab="Heterozygosity of individuals")
hist(het.snp,col="gray", main="",ylab=ylab.snp, xlab="Heterozygosity of markers")
dev.off()
rm(X, H, het.ind, het.snp) #Feree memory
myFig21<-myGI
myFig21<-myFig21[!is.na(as.numeric(as.matrix(myFig21[,3]))),]
n<-nrow(myFig21)
maxchr<-0
for(i in 1:n){
if(as.numeric(as.matrix(myFig21[i,2]))>maxchr){
maxchr<-as.numeric(as.matrix(myFig21[i,2]))
}
}
n_end<-maxchr
if(maxchr==0){
chr=0
}
#n_end<-as.numeric(as.matrix(myFig21[n,2]))
aaa<-NULL
for(i in 0:n_end){
#myChr<-myFig21[myFig21[,2]==i,]
myChr<-myFig21[as.numeric(as.matrix(myFig21[,2]))==i,]
index<-order(as.numeric(as.matrix(as.data.frame(myChr[,3]))))
aaa<-rbind(aaa,myChr[index,])
}
myFig2<-aaa
if(is.null(w1_end)){
if(nrow(myFig2[as.numeric(as.matrix(myFig2[,2]))==chr,])>100){
w1_end=100
}else{
w1_end=nrow(myFig2[as.numeric(as.matrix(myFig2[,2]))==chr,])
}
}
subResult<-matrix(0,n,1)
for(i in 1 :( n-1))
{
k<-as.numeric(as.matrix(myFig2[i+1,3]))-as.numeric(as.matrix(myFig2[i,3]))
if(k>0){
subResult[i]<-k
}
else{
subResult[i]<-0
}}
results<-cbind(myFig2,subResult)
#####Out Distribution of SNP density ##########
#####Out Accumulation##########
kk0<-order(as.numeric(as.matrix(results[,4])))
myFig22<-results[kk0,]
m<-nrow(myFig22)
kk1<-matrix(1:m,m,1)
results2<-cbind(myFig22,kk1)
max2<-max(myFig22[,4])
pdf("GAPIT.Marker.Density.pdf", width =10, height = 6)
par(mar=c(5,5,4,5)+0.1)
hist(as.numeric(as.matrix(results[,4])),xlab="Density",main="Distribution of SNP",breaks=12, cex.axis=0.9,col = "dimgray",cex.lab=1.3)###,xlim=c(0,25040359))
par(new=T)
plot(results2[,4],results2[,5]/m,xaxt="n", yaxt="n",bg="lightgray",xlab="",ylab="",type="l",pch=20,col="#990000",cex=1.0,cex.lab=1.3, cex.axis=0.9, lwd=3,las=1,xlim=c(0,max2))
axis(4,col="#990000",col.ticks="#990000",col.axis="#990000")
mtext("Accumulation Frequency",side=4,line=3,font=2,font.axis=1.3,col="#990000")
abline(h=0,col="forestgreen",lty=2)
abline(h=1,col="forestgreen",lty=2)
dev.off()
#####Out Moving Average of density##########
#print(unique(myGI[,2]))
myGD0<-myGD[,as.numeric(myGI[,2])==chr]
gc()
myGM0<-myGI[myGI[,2]==chr,]
##remove invalid SNPs
#X<-myGD0[,-1]
X<-myGD0
colMax=apply(X,2,max)
colMin=apply(X,2,min)
#mono=as.numeric(colMax)-as.numeric(colMin)
mono=colMax-colMin
index=mono<10E-5
X=X[,!index]
myFig3<-myGM0[!index,]
n3<-nrow(myFig3)
kk3<-order(as.numeric(as.matrix(myFig3[,3])))
myFig23<-myFig3[kk3,]
myGD3<-X[,kk3]
##set windows long
##w1_start<-30
##w1_end<-230
###get windows numeric snp at the same chr
#print(w1_start)
#print(w1_end)
#print(dim(myFig3))
if(nrow(myFig23)<w1_end)w1_end=nrow(myFig23)
#print(w1_start)
#print(w1_end)
results3_100<-myFig23[w1_start:w1_end,]
myGD3_100<-myGD3[,w1_start:w1_end]
km<-w1_end-w1_start+1
##get number of Density about snp
sum_number_Density <-0
for(j in 1:km)
{
sum_number_Density<-sum_number_Density+(j-1)
}
save_Density_Cor<-matrix(0.0,sum_number_Density,3)
save_Density_Cor_name<-matrix("",sum_number_Density,1)
countSDC<-1
for(j in 1:(km-1))
{
for(k in (j+1):km)
{
save_Density_Cor[countSDC,1]<-abs(as.numeric(as.matrix(results3_100[k,3]))-as.numeric(as.matrix(results3_100[j,3])))
save_Density_Cor[countSDC,2]<-cor(myGD3_100[,j],myGD3_100[,k])
#options(digits=8)
#save_Density_Cor[countSDC,3]<-as.numeric(as.matrix(format(cor(myGD3_100[,j],myGD3_100[,k])%*% cor(myGD3_100[,j],myGD3_100[,k]),digits=8)))
save_Density_Cor[countSDC,3]<-cor(myGD3_100[,j],myGD3_100[,k])%*% cor(myGD3_100[,j],myGD3_100[,k])
save_Density_Cor_name[countSDC,1]<-paste(results3_100[j,1],"::::",results3_100[k,1],seq="")
countSDC<-countSDC+1
}
}
#result3_30<-as.data.frame(cbind(save_Density_Cor_name,save_Density_Cor))
k3_3<-order(save_Density_Cor[,1])
result3_3<-save_Density_Cor[k3_3,]
##set moving average value
##mav1<-100
result_mav2<-matrix(0.0,sum_number_Density-mav1,1)
mav1_1<-floor(mav1/2)
mav1_1_end<-sum_number_Density-mav1+mav1_1
result_mav1<-result3_3[(mav1_1+1):mav1_1_end,1]
for(g in 1:(sum_number_Density-mav1)){
sum<-0
for(i in g:(g+mav1-1)){
sum<-sum+result3_3[i,3]
}
#result_mav2[g]<-sum/mav1*5
result_mav2[g]<-sum/mav1
}
result_mav<-cbind(result_mav1,result_mav2)
pdf("GAPIT.Marker.LD.pdf", width =10, height = 6)
par(mar = c(5,5,5,5))
plot(as.matrix(result3_3[,1]),as.matrix(result3_3[,3]),bg="dimgray",xlab="Distance",ylab="R Square",pch=1,cex=0.9,cex.lab=1.2, lwd=0.75,las=1)
#,ylim=c(0,round(max(result3_3[,3]))))
lines(result_mav[,2]~result_mav[,1], lwd=6,type="l",pch=20,col="#990000")
dev.off()
print(paste("GAPIT.Genotype.View ", ".Two pdf generate.","successfully!" ,sep = ""))
#GAPIT.Genotype.View
}
#=============================================================================================
`GAPIT.HMP2Num` <-
function(nLines=n,fileHMP="hmp.txt",fileNum="num.txt",bit=1,SNP.effect="Add",SNP.impute="Middle",heading=TRUE, Create.indicator = FALSE, Major.allele.zero = FALSE){
#Object: To convert hmp file to numerical file
#Input: hmp genotype file
#Output: Numerical genotype file
#Authors: Zhiwu Zhang
# Last update: May 23, 2013
##############################################################################################
#print("GAPIT.HMP2Num start")
setwd("/Users/Zhiwu/Dropbox/Current/paper/BigData/BUS/Robust/MaizeGBS")
fileHMP="NAMs26HM2.c10.imp.hmp.txt"
fileNum="NAMs26HM2.c10s.imp.num.txt"
bit=1
SNP.effect="Add"
SNP.impute="Middle"
Major.allele.zero = FALSE
system.time({
n=2000
fileHMPCon<-file(fileHMP, open="r")
#fileNumCon<-file(fileNum, open="r")
tt<-readLines(fileHMPCon, n=1) #header
for(i in 1:n){
if(i %% 100 == 0)print(i)
tt<-readLines(fileHMPCon, n=1)
#tt2<-na.omit(as.numeric(unlist(strsplit(tt, "\t"))))
tt2<-unlist(strsplit(tt, "\t"))
#GM
rs=tt2[1]
chrom=tt2[3]
pos=tt2[4]
#GD
GD= GAPIT.Numericalization(x=tt2[-c(1:11)],bit=bit,effect=SNP.effect,impute=SNP.impute, Major.allele.zero=Major.allele.zero)
#Output
#print(i)
#print(tt2[12:52])
#print(GD[1:41])
#writeLines(tt2, fileNumCon,append=TRUE)
}
close.connection(fileHMPCon)
})
#print("GAPIT.HMP2Num accomplished successfully!")
} #GAPIT.HMP2Num ends here
#=============================================================================================
`GAPIT.HapMap` <-
function(G,SNP.effect="Add",SNP.impute="Middle",heading=TRUE, Create.indicator = FALSE, Major.allele.zero = FALSE){
#Object: To convert character SNP genotpe to numerical
#Output: Coresponding numerical value
#Authors: Feng Tian and Zhiwu Zhang
# Last update: May 30, 2011
##############################################################################################
print(paste("Converting HapMap format to numerical under model of ", SNP.impute,sep=""))
#gc()
#GAPIT.Memory.Object(name.of.trait="HapMap.Start")
#GT=data.frame(G[1,-(1:11)])
if(heading){
GT= t(G[1,-(1:11)])
GI= G[-1,c(1,3,4)]
}else{
GT=NULL
GI= G[,c(1,3,4)]
}
#Set column names
if(heading)colnames(GT)="taxa"
colnames(GI)=c("SNP","Chromosome","Position")
#Initial GD
GD=NULL
bit=nchar(as.character(G[2,12])) #to determine number of bits of genotype
#print(paste("Number of bits for genotype: ", bit))
print("Perform numericalization")
if(heading){
if(!Create.indicator) GD= apply(G[-1,-(1:11)],1,function(one) GAPIT.Numericalization(one,bit=bit,effect=SNP.effect,impute=SNP.impute, Major.allele.zero=Major.allele.zero))
if(Create.indicator) GD= t(G[-1,-(1:11)])
}else{
if(!Create.indicator) GD= apply(G[ ,-(1:11)],1,function(one) GAPIT.Numericalization(one,bit=bit,effect=SNP.effect,impute=SNP.impute, Major.allele.zero=Major.allele.zero))
if(Create.indicator) GD= t(G[ ,-(1:11)])
}
#set GT and GI to NULL in case of null GD
if(is.null(GD)){
GT=NULL
GI=NULL
}
#print("The dimension of GD is:")
#print(dim(GD))
if(!Create.indicator) {print(paste("Succesfuly finished converting HapMap which has bits of ", bit,sep="")) }
return(list(GT=GT,GD=GD,GI=GI))
}#end of GAPIT.HapMap function
#=============================================================================================
`GAPIT.IC` <-
function(DP=NULL){
#Object: To Intermediate Components
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("GAPIT.IC in process...")
Y=DP$Y
PC=DP$PC
CV=DP$CV
GD=DP$GD
noCV=FALSE
if(is.null(CV)){
noCV=TRUE
CV=Y[,1:2]
CV[,2]=1
colnames(CV)=c("taxa","overall")
print(paste("There is 0 Covarinces.",sep=""))
}
taxa_Y=as.character(Y[,1])
taxa_GD=as.character(GD[,1])
if(DP$PCA.total>0&!is.null(DP$CV))CV=GAPIT.CVMergePC(DP$CV,PC)
if(DP$PCA.total>0&is.null(DP$CV))CV=PC
taxa_comGD=as.character(GD[,1])
taxa_comY=as.character(Y[,1])
taxa_CV=as.character(CV[,1])
taxa_comall=intersect(intersect(taxa_comGD,taxa_comY),taxa_CV)
comCV=CV[taxa_CV%in%taxa_comall,]
comGD=GD[taxa_comGD%in%taxa_comall,]
comY=Y[taxa_comY%in%taxa_comall,]
GT=as.matrix(as.character(taxa_comall))
print(paste("There are ",length(GT)," common individuals in genotype , phenotype and CV files.",sep=""))
if(nrow(comCV)!=length(GT))stop ("GAPIT says: The number of individuals in CV does not match to the number of individuals in genotype files.")
print("The dimension of total CV is ")
print(dim(comCV))
print("GAPIT.IC accomplished successfully for multiple traits. Results are saved")
if(DP$kinship.algorithm%in%c("FarmCPU","Blink","MLMM")){
return (list(Y=comY,GT=GT,PCA=comCV,K=DP$KI,GD=comGD,GM=DP$GM,myallCV=CV,myallGD=GD))
}else{
return (list(Y=comY,GT=GT,PCA=comCV,K=DP$KI,GD=comGD,GM=DP$GM,myallCV=CV,myallGD=GD,myallY=Y))
}
} #end of GAPIT IC function
#=============================================================================================
`GAPIT.ID` <-
function(DP=NULL,IC=NULL,SS=NULL,RS=NULL,cutOff=0.01,
DPP=100000,Create.indicator=FALSE,
FDR.Rate = 1,QTN.position=NULL,plot.style="Oceanic",
file.output=TRUE,SNP.MAF=0,CG=NULL,plot.bin=10^9 ){
#Object: To Interpretation and Diagnoses
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("GAPIT.ID in process...")
#Define the funcitno here
if(is.null(DP)&is.null(IC))#inputdata is other method result
{
GWAS=RS
GI=RS[,1:3]
GI=GI[order(GI[,2]),]
GI=GI[order(GI[,1]),]
#print(QTN.position)
ps=RS[,4]
nobs=nrow(RS)
if(ncol(RS)>4)
{maf=RS[,5]
maf_pass=TRUE
}
if(ncol(RS)<5)
{maf_pass=FALSE
maf=0.5
}
rsquare_base=rep(NA,length(ps))
rsquare=rep(NA,length(ps))
df=rep(NA,length(nobs))
tvalue=rep(NA,length(nobs))
stderr=rep(NA,length(nobs))
effect.est=rep(NA,length(nobs))
if(is.na(maf[1])) maf=matrix(.5,nrow(GWAS),1)
print("Filtering SNPs with MAF..." )
index=maf>=SNP.MAF
PWI.Filtered=cbind(GI,ps,maf,nobs,rsquare_base,rsquare)#[index,]
colnames(PWI.Filtered)=c("SNP","Chromosome","Position ","P.value", "maf", "nobs", "Rsquare.of.Model.without.SNP","Rsquare.of.Model.with.SNP")
if(!is.null(PWI.Filtered))
{
print("Calculating FDR..." )
PWIP <- GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure(PWI = PWI.Filtered, FDR.Rate = FDR.Rate, FDR.Procedure = "BH")
print("QQ plot..." )
if(file.output) GAPIT.QQ(P.values = ps, name.of.trait = name.of.trait,DPP=DPP)
print("Manhattan plot (Genomewise)..." )
if(file.output) GAPIT.Manhattan(GI.MP = cbind(GI[,-1],ps), name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff,seqQTN=QTN.position,plot.style=plot.style,plot.bin=plot.bin)
print("Manhattan plot (Chromosomewise)..." )
#if(file.output) GAPIT.Manhattan(GI.MP = PWIP$PWIP[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Chromosomewise",cutOff=cutOff)
if(file.output) GAPIT.Manhattan(GI.MP = cbind(GI[,-1],ps), name.of.trait = name.of.trait, DPP=DPP, plot.type = "Chromosomewise",cutOff=cutOff,plot.bin=plot.bin)
#Association Table
print("Association table..." )
#GAPIT.Table(final.table = PWIP$PWIP, name.of.trait = name.of.trait,SNP.FDR=SNP.FDR)
# GWAS=PWIP$PWIP[PWIP$PWIP[,9]<=DP$SNP.FDR,]
# print(head(GWAS))
print("Joining tvalue and stderr" )
DTS=cbind(GI,df,tvalue,stderr,effect.est)
colnames(DTS)=c("SNP","Chromosome","Position","DF","t Value","std Error","effect")
print("Creating ROC table and plot" )
if(file.output) myROC=GAPIT.ROC(t=tvalue,se=stderr,Vp=var(ys),trait=name.of.trait)
print("ROC table and plot created" )
print("MAF plot..." )
if(file.output&maf_pass) myMAF1=GAPIT.MAF(MAF=maf,P=ps,E=NULL,trait=name.of.trait)
if(file.output){
write.table(GWAS, paste("GAPIT.", name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
write.table(DTS, paste("GAPIT.", name.of.trait, ".Df.tValue.StdErr.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#if(!byPass) write.table(GWAS.2, paste("GAPIT.", name.of.trait, ".Allelic_Effect_Estimates.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}#end file.output
}#end DP
}else{ #inputdata is GAPIT3 result
name.of.trait=DP$memo
GWAS=SS$GWAS
#print(head(GWAS))
Pred=SS$Pred
GI=GWAS
GI=GI[order(GI[,3]),]
GI=GI[order(GI[,2]),]
byPass=TRUE
if(DP$kinship.algorithm%in%c("FarmCPU","MLMM","Blink"))byPass=FALSE
if(byPass)
{
# print(head(SS$GWAS))
ps=SS$TV$ps
nobs=SS$TV$nobs
maf=GWAS$maf
#maf=SS$TV$maf
rsquare_base=SS$TV$rsquare_base
rsquare=SS$TV$rsquare
df=SS$TV$df
tvalue=SS$TV$tvalue
stderr=SS$TV$stderr
effect.est=SS$mc
effect=SS$mc
#GI=cbind(GI,effect)
if(DP$file.output&!is.null(SS$Compression)&!is.na(SS$Compression[1,6])) GAPIT.Compression.Visualization(Compression = SS$Compression, name.of.trait = DP$name.of.trait)
}else{
maf=GI$maf
ps=GI$P.value
nobs=GI$nobs
rsquare_base=rep(NA,length(ps))
rsquare=rep(NA,length(ps))
df=rep(NA,length(nobs))
tvalue=rep(NA,length(nobs))
stderr=rep(NA,length(nobs))
effect.est=GI$effect
}
if(is.na(maf[1])) maf=matrix(.5,nrow(GI),1)
if(!is.null(IC$GD)&DP$SNP.test)
{
print("Filtering SNPs with MAF..." )
#index=maf>=DP$SNP.MAF
#PWI.Filtered=cbind(GI[,-5],rsquare_base,rsquare)
PWI.Filtered=cbind(GWAS[,1:6],rsquare_base,rsquare)
colnames(PWI.Filtered)=c("SNP","Chromosome","Position ","P.value", "maf", "nobs", "Rsquare.of.Model.without.SNP","Rsquare.of.Model.with.SNP")
if(!is.null(PWI.Filtered))
{
#Run the BH multiple correction procedure of the results
#Create PWIP, which is a table of SNP Names, Chromosome, bp Position, Raw P-values, FDR Adjusted P-values
print("Calculating FDR..." )
PWIP <- GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure(PWI = PWI.Filtered, FDR.Rate = FDR.Rate, FDR.Procedure = "BH")
#print(str(PWIP))
print("QQ plot..." )
if(DP$file.output) GAPIT.QQ(P.values = GI$P.value, name.of.trait = DP$name.of.trait,DPP=DP$DPP)
print("Manhattan plot (Genomewise)..." )
if(DP$file.output) GAPIT.Manhattan(GI.MP = GWAS[,2:4], name.of.trait = DP$name.of.trait, DPP=DP$DPP, plot.type = "Genomewise",cutOff=DP$cutOff,seqQTN=DP$QTN.position,plot.style=DP$plot.style,plot.bin=DP$plot.bin,chor_taxa=DP$chor_taxa)
#print("@@@@@@@@@@@@@@@@@@@@@@@@")
print("Manhattan plot (Chromosomewise)..." )
if(DP$file.output) GAPIT.Manhattan(GI.MP = GWAS[,2:4],GD=IC$GD[,-1], CG=DP$CG,name.of.trait = DP$name.of.trait, DPP=DP$DPP, plot.type = "Chromosomewise",cutOff=DP$cutOff,plot.bin=DP$plot.bin)
#Association Table
print("Association table..." )
print("Joining tvalue and stderr" )
# print(head(GWAS))
# print(length(df))
# print(length(tvalue))
# print(length(stderr))
# print(length(effect.est))
DTS=cbind(GWAS[,1:3],df,tvalue,stderr,effect.est)
colnames(DTS)=c("SNP","Chromosome","Position","DF","t Value","std Error","effect")
print("Creating ROC table and plot" )
if(DP$file.output) myROC=GAPIT.ROC(t=tvalue,se=stderr,Vp=var(as.matrix(DP$Y[,2])),trait=DP$name.of.trait)
print("ROC table and plot created" )
print("MAF plot..." )
if(DP$file.output) myMAF1=GAPIT.MAF(MAF=maf,P=ps,E=NULL,trait=DP$name.of.trait)
print("GAPIT.Interactive.Manhattan")
print(DP$Inter.type)
#GI=GI[order(GI[,4]),]
#print(head(GI))
if(ncol(GI)>1)
{new_GI=merge(PWIP$PWIP,GI[,c("SNP","effect")],by.x="SNP",by.y="SNP")
}else{
new_GI=GI
}
new_GI=new_GI[order(new_GI[,4]),]
#print(head(new_GI))
if(DP$file.output&DP$Inter.Plot) GAPIT.Interactive.Manhattan(GWAS=new_GI,X_fre=maf,plot.type=DP$Inter.type,name.of.trait = DP$name.of.trait)
if(DP$file.output){
write.table(new_GI, paste("GAPIT.", DP$name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
write.table(DTS, paste("GAPIT.", DP$name.of.trait, ".Df.tValue.StdErr.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#print(head(GWAS.2))
#if(byPass) write.table(GWAS.2[,1:4], paste("GAPIT.", DP$name.of.trait, ".Allelic_Effect_Estimates.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}#end file.output
}#PWI.Filtered
}#end IC$GD)
print("GAPIT.ID accomplished successfully for multiple traits. Results are saved")
return ()
}#is.null(DP)&is.null(IC)
} #end of GAPIT.ID function
#=============================================================================================
`GAPIT.Imputation` <-
function(x,GI=NULL,impute="Middle",byRow=TRUE){
#Object: To impute NA in genome
#Output: Coresponding numerical value
#Authors: Zhiwu Zhang
#Writer: Jiabo Wang
# Last update: April 13, 2016
##############################################################################################
n=length(x)
lev=levels(as.factor(x))
lev=setdiff(lev,NA)
#print(lev)
len=length(lev)
count=1:len
for(i in 1:len){
count[i]=length(x[(x==lev[i])])
}
position=order(count)
#print(position)
if(impute=="Middle") {x[is.na(x)]=1 }
if(len==3){
if(impute=="Minor") {x[is.na(x)]=position[1] -1}
if(impute=="Major") {x[is.na(x)]=position[len]-1}
}else{
if(impute=="Minor") {x[is.na(x)]=2*(position[1] -1)}
if(impute=="Major") {x[is.na(x)]=2*(position[len]-1)}
}
if(byRow) {
result=matrix(x,n,1)
}else{
result=matrix(x,1,n)
}
return(result)
}#end of GAPIT.Numericalization function
#=============================================================================================
`GAPIT.Interactive.GS`<-
function(model_store=NULL,Y=NULL,myGD=NULL,myGM=NULL,myKI=NULL,myY=NULL,myCV=NULL,rel=NULL,h2=NULL,NQTN=NULL
)
#model_store is the store of all model names
#Y is the real phenotype
#
{
# e=20
# #NQTN=100
# #h2=0.25
# taxa=as.character(myGD[,1])
# myY=Y0[Y0[,1]%in%taxa,c(1,e)]
# myGD=myGD[taxa%in%myY[,1],]
# nfold=5
# repli=1
# sets=sample(cut(1:nrow(myY ),nfold,labels=FALSE),nrow(myY ))
# j=1
# training=myY
# training[sets==j,2]=NA
# training_index=is.na(training[,2])
# testing=myY[training_index,]
# cblup_gapit=GAPIT(Y=training,CV=PC,PCA.total=0,KI=myKI,group.from=200,group.to=2000,group.by=600,SNP.test=F,file.output=F)
# gblup_gapit=GAPIT(Y=training,CV=PC,PCA.total=0,KI=myKI,group.from=2000,group.to=2000,group.by=100,SNP.test=F,file.output=F)
# sblup_gapit=GAPIT(Y=training,CV=PC,PCA.total=0,GD=myGD,GM=myGM,group.from=2000,SUPER_GS=TRUE,sangwich.top="MLM",sangwich.bottom="SUPER",LD=0.1,SNP.test=F,file.output=F,inclosure.from=200,inclosure.to=1000,inclosure.by=200,bin.from=10000,bin.to=100000,bin.by=10000)
# cblup_pred=cblup_gapit$Pred[training_index,]
# gblup_pred=gblup_gapit$Pred[training_index,]
# sblup_pred=sblup_gapit$Pred[training_index,]
# testing_index=!is.na(testing[,2])
# gblup_r_once=cor(testing[testing_index,2],gblup_pred[testing_index,8])
# cblup_r_once=cor(testing[testing_index,2],cblup_pred[testing_index,8])
# sblup_r_once=cor(testing[testing_index,2],sblup_pred[testing_index,8])
# result=cbind(testing[testing_index,],gblup_pred[testing_index,8],cblup_pred[testing_index,8],sblup_pred[testing_index,8])
# colnames(result)=c("taxa","observed","gBLUP","cBLUP","sBLUP")
# gblup_r_once
# cblup_r_once
# sblup_r_once
# write.table(result,paste("gcs_",e,".txt",sep=""))
myY=read.table(paste("gcs_",e,".txt",sep=""),head=T)
Observed=myY$observed
Predicted=myY$gBLUP
if(!require(plotly)) install.packages("plotly")
library(plotly)
p <- plot_ly(
type = 'scatter',
x = ~Observed,
y = ~Predicted,
data=myY,
text = ~paste("Taxa: ",taxa,"<br>Observed: ",round(observed,4) , '<br>gBLUP:', round(gBLUP,4)),
#size=2*y/max(y),
color = I("red"),
name=c("gBLUP")
)%>%add_trace(
type = 'scatter',
x = ~observed,
y = ~cBLUP,
#data=myY,
text = ~paste("Taxa: ",taxa,"<br>Observed: ",round(observed,4) , '<br>cBLUP:', round(cBLUP,4)),
#size=2*y/max(y),
color = I("blue"),
name=c("cBLUP")
)%>%add_trace(
type = 'scatter',
x = ~observed,
y = ~sBLUP,
#data=myY,
text = ~paste("Taxa: ",taxa,"<br>Observed: ",round(observed,4) , '<br>sBLUP:', round(sBLUP,4)),
#size=2*y/max(y),
color = I("green"),
name=c("sBLUP")
)
htmltools::save_html(p, "Interactive.GS.html")
}
`GAPIT.Interactive.Manhattan`<-
function(GWAS=NULL,MAF.threshold=seq(0,0.5,.1),cutOff=0.01,DPP=50000,X_fre=NULL,plot.type=c("m","q"),name.of.trait = "Trait"
)
{
if(is.null(GWAS)) stop("Please add GWAS result in here!!!")
MP=GWAS[,2:4]
#print(head(GWAS))
GWAS=GWAS[order(GWAS[,3]),]
GWAS=GWAS[order(GWAS[,2]),]
#print(GWAS[GWAS[,4]==min(GWAS[,4]),2])
taxa=as.character(GWAS[,1])
numMarker=nrow(GWAS)
bonferroniCutOff01=-log10(0.01/numMarker)
bonferroniCutOff05=-log10(0.05/numMarker)
# deal with P value to log
Ps=as.numeric(as.vector(GWAS[,4]))
logPs <- -log10(Ps)
logPs[is.na(logPs)]=0
y.lim <- ceiling(max(GWAS[,4]))
chrom_total=as.numeric(as.character((GWAS[,2])))
#print(GWAS[GWAS[,4]==min(GWAS[,4]),])
#print("!!!!")
#print(chrom_total[logPs==max(logPs)])
POS=as.numeric(as.vector(GWAS[,3]))
#print(head(POS))
chm.to.analyze <- as.numeric(as.character(unique(GWAS[,2])))
chm.to.analyze=chm.to.analyze[order(as.numeric(as.character(chm.to.analyze)))]
#chm.to.analyze = factor(sort(chm.to.analyze))
numCHR= length(chm.to.analyze)
print(chm.to.analyze)
ticks=NULL
lastbase=0
#change base position to accumulatives (ticks)
for (i in chm.to.analyze)
{
index=(chrom_total==i)
ticks <- c(ticks, lastbase+mean(POS[index]))
POS[index]=POS[index]+lastbase
lastbase=max(POS[index])
}
x0 <- POS
y0 <- as.numeric(logPs)
z0 <- chrom_total
posi0<-as.numeric(as.vector(GWAS$Position))
maf0 <- as.numeric(as.vector(GWAS$maf))
effect0<- as.numeric(as.vector(GWAS$effect))
#print(head(z0))
position=order(y0,decreasing = TRUE)
index0=GAPIT.Pruning(y0[position],DPP=DPP)
index=position[index0]
#order by P value
x=x0[index]
y=y0[index]
z=z0[index]
taxa=taxa[index]
posi=posi0[index]
maf=maf0[index]
effect=effect0[index]
plot.color=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(numCHR/5))
if(c("m")%in%plot.type)
{
Position=x
P_value=y
z[z<10]=paste("0",z[z<10],sep="")
zz=paste("Chr_",z,sep="")
#print(zz)
if(!require(plotly)) install.packages("plotly")
#print("!!!!!")
#print(head(Position))
library(plotly)
p <- plot_ly(
type = 'scatter',
x = ~Position,
y = ~P_value,
colorscale='Viridis',
reversescale =T,
#symbol="circle",
text = ~paste("SNP: ", taxa, "<br>Posi: ", posi,"<br>MAF: ", round(maf,2),"<br>Effect: ",round(effect,2)),
color = ~as.character(zz)
)%>%
add_trace(y=bonferroniCutOff01,name = 'CutOff-0.01',color=I("red"),mode="line",width=1.4,text="")%>%
add_trace(y=bonferroniCutOff05,name = 'CutOff-0.05',color=I("red"),mode="line",line=list(width=1.4,dash='dot'),text="")%>%
layout(title = "Interactive.Manhattan.Plot",
#showticklabels = FALSE,
#legend = list(orientation = 'h'),
xaxis = list(title = "Chromsome",zeroline = FALSE,showticklabels = FALSE),
yaxis = list (title = "-Log10(p)"))
htmltools::save_html(p, paste("Interactive.Manhattan.",name.of.trait,".html",sep=""))
}
################ for QQ plot
if(c("q")%in%plot.type)
{
P.values=y
p_value_quantiles <- (1:length(P.values))/(length(P.values)+1)
log.P.values <- P.values
log.Quantiles <- -log10(p_value_quantiles)
index=GAPIT.Pruning(log.P.values,DPP=DPP)
log.P.values=log.P.values[index ]
log.Quantiles=log.Quantiles[index]
N=length(P.values)
N1=length(log.Quantiles)
## create the confidence intervals
c95 <- rep(NA,N1)
c05 <- rep(NA,N1)
for(j in 1:N1){
i=ceiling((10^-log.Quantiles[j])*N)
if(i==0)i=1
c95[j] <- qbeta(0.95,i,N-i+1)
c05[j] <- qbeta(0.05,i,N-i+1)
#print(c(j,i,c95[j],c05[j]))
}
#CI shade
#plot3d(NULL, xlim = c(0,max(log.Quantiles)), zlim = c(0,max(log.P.values)), type="l",lty=5, lwd = 2, axes=FALSE, xlab="", ylab="",col="gray")
index=length(c95):1
zz=paste("Chr_",z,sep="")
Expected=log.Quantiles
Observed=log.P.values
#abline(a = 0, b = 1, col = "red",lwd=2)
qp <- plot_ly(
type = 'scatter',
x = ~Expected,
y = ~Observed,
text = ~paste("SNP: ", taxa,"<br>Chr: ",zz,"<br>Posi: ", posi, "<br>MAF: ", round(maf,2),"<br>Effect: ",round(effect,2)),
#size=2*y/max(y),
name = "SNP",
opacity=0.5,
)%>%add_lines(x=log.Quantiles,y=log.Quantiles,color=I("red"),
mode = 'lines',name="Diag",text="")%>%
layout(title = "Interactive.QQ.Plot",
xaxis = list(title = "Expected -Log10(p)"),
yaxis = list (title = "Observed -Log10(p)"),
#showticklabels = FALSE,
showlegend = FALSE)
htmltools::save_html(qp, paste("Interactive.QQ ",name.of.trait,".html",sep=""))
}
print("GAPIT.Interactive.Plot has done !!!")
}#end of GAPIT.Interactive.Manhattan
#=============================================================================================
`GAPIT.Judge`<-
function(Y=Y,G=NULL,GD=NULL,KI=NULL,GM=NULL,group.to=group.to,group.from=group.from,sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,kinship.algorithm=kinship.algorithm,PCA.total=PCA.total,model="MLM",SNP.test=TRUE){
#Object: To judge Pheno and Geno data practicability
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("--------------------Phenotype and Genotype ----------------------------------")
if(ncol(Y)<2) stop ("Phenotype should have taxa name and one trait at least. Please correct phenotype file!")
print(kinship.algorithm)
if(is.null(KI)&is.null(GD) & kinship.algorithm!="SUPER"&is.null(G)) stop ("GAPIT says: Kinship is required. As genotype is not provided, kinship can not be created.")
if(kinship.algorithm=="FarmCPU"&SNP.test==FALSE)stop("FarmCPU is only for GWAS, plase set: SNP.test= TRUE")
#if((!is.null(GD))&(!is.null(G))) stop("GAPIT Says:Please put in only one type of geno data.")
if(is.null(GD)&is.null(G)&is.null(KI))stop ("GAPIT Says:GAPIT need genotype!!!")
if(!is.null(GD) & is.null(GM) & (is.null(G)) &SNP.test) stop("GAPIT Says: Genotype data and map files should be in pair")
if(is.null(GD) & !is.null(GM) & (is.null(G)) &SNP.test) stop("GAPIT Says: Genotype data and map files should be in pair")
if (is.null(GD[,1]%in%Y[,1])|is.null(colnames(G)[-c(1:11)]%in%Y[,1]))stop("GAPIT Says: There are no common taxa between genotype and phenotype")
if (!is.null(Y)) nY=nrow(Y)
if (!is.null(Y)) ntrait=ncol(Y)-1
print(paste("There are ",ntrait," traits in phenotype data."))
print(paste("There are ",nY," individuals in phenotype data."))
if (!is.null(G)) nG=nrow(G)-11
if (!is.null(GD))
{nG=ncol(GD)-1
print(paste("There are ",nG," markers in genotype data."))}
print("Phenotype and Genotype are test OK !!")
print("--------------------GAPIT Logical ----------------------------------")
#if (group.to>nY&is.null(KI))group.to=nY
#if (group.from>group.to&is.null(KI)) group.from=group.to
if(!is.null(sangwich.top) & is.null(sangwich.bottom) ) stop("GAPIT Says: SUPER method need sangwich.top and bottom")
if(is.null(sangwich.top) & !is.null(sangwich.bottom) ) stop("GAPIT Says: SUPER method need sangwich.top and bottom")
if(kinship.algorithm=="Separation"&PCA.total==0) stop ("GAPIT Says: Separation kinship need PCA.total>0")
return (list(group.to=group.to,group.from=group.from))
}#end of GAPIT.Pheno.Geno.judge function
#=============================================================================================
`GAPIT.Liner` <-
function(Y,GD,CV){
#Object: To have Y, GD and CV the same size and order
#Input: Y,GDP,GM,CV
#Input: GD - n by m +1 dataframe or n by m big.matrix
#Input: GDP - n by m matrix. This is Genotype Data Pure (GDP). THERE IS NOT COLUMN FOR TAXA.
#Input: orientation-Marker in GDP go colmun or row wise
#Requirement: Y, GDP and CV have same taxa order. GDP and GM have the same order on SNP
#Output: GWAS,GPS,Pred
#Authors: Zhiwu Zhang
# Last update: Febuary 24, 2013
##############################################################################################
#print("GAPIT.Liner Started")
#print(date())
#print("Memory used at begining of BUS")
#print(memory.size())
#print("dimension of Y,GD and CV at begining")
#print(dim(Y))
#print(dim(GD))
#print(dim(CV))
if(!is.null(CV))taxa=intersect(intersect(GD[,1],Y[,1]),CV[,1])
if(is.null(CV))taxa=intersect(GD[,1],Y[,1])
Y=Y[match(taxa, Y[,1], nomatch = 0),]
GD=GD[match(taxa, GD[,1], nomatch = 0),]
if(!is.null(CV)) CV=CV[match(taxa, CV[,1], nomatch = 0),]
Y = Y[order(Y[,1]),]
GD = GD[order(GD[,1]),]
if(!is.null(CV)) CV = CV[order(CV[,1]),]
#print("dimension of Y,GD and CV at end")
#print(dim(Y))
#print(dim(GD))
#print(dim(CV))
print("GAPIT.Liner accomplished successfully")
return (list(Y=Y,GD=GD,CV=CV))
}#The function GAPIT.Liner ends here
#=============================================================================================
`GAPIT.Log` <-
function(Y=Y,KI=KI,Z=Z,CV=CV,SNP.P3D=SNP.P3D,
group.from = group.from ,group.to =group.to ,group.by = group.by ,kinship.cluster = kinship.cluster, kinship.group= kinship.group,
ngrid = ngrid , llin = llin , ulim = ulim , esp = esp ,name.of.trait = name.of.trait){
#Object: To report model factors
#Output: Text file (GAPIT.Log.txt)
#Authors: Zhiwu Zhang
# Last update: may 16, 2011
##############################################################################################
#Creat storage
facto <- list(NULL)
value <- list(NULL)
#collecting model factors
facto[[1]]="Trait"
value[[1]]=paste(dim(Y))
facto[[2]]="group.by "
value[[2]]=group.by
facto[[3]]="Trait name "
value[[3]]=name.of.trait
facto[[4]]="Kinship"
value[[4]]=dim(KI)
facto[[5]]="Z Matrix"
value[[5]]=dim(Z)
facto[[6]]="Covariate"
value[[6]]=dim(CV)
facto[[7]]="SNP.P3D"
value[[7]]=SNP.P3D
facto[[8]]="Clustering algorithms"
value[[8]]=kinship.cluster
facto[[9]]="Group kinship"
value[[9]]=kinship.group
facto[[10]]="group.from "
value[[10]]=group.from
facto[[11]]="group.to "
value[[11]]=group.to
theLog=as.matrix(cbind(facto,value))
#theLog=as.character(as.matrix(cbind(facto,value)))
colnames(theLog)=c("Model", "Value")
file=paste("GAPIT.", name.of.trait,".Log.csv" ,sep = "")
write.table(theLog, file, quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
return (theLog)
}
#=============================================================================================
`GAPIT.MAF` <-
function(MAF=NULL,P=NULL,E=NULL,trait="",threshold.output=.1,plot.style="rainbow"){
#Object: To display probability and effect over MAF
#Input: MAF vector of MAF
#Input: P vector of P values
#Output: A table and plot
#Requirment: NA
#Authors: Zhiwu Zhang
# Start date: April 5, 2013
# Last update: Oct 27, 2015 by Jiabo Wang add notice for P<0.1 is empty
##############################################################################################
#print("MAF plot started")
#print(threshold.output)
#Remove NAs and under threshold
index= which(P<threshold.output & !is.na(MAF))
MAF=MAF[index]
#E=E[index]
P=P[index]
LP=-log10(P)
LPC=round(LP*10,digits = 0)+20
ncolors=max(LPC,na.rm=T)
if(ncolors > 1024) {ncolors=1024}
if(ncolors==-Inf)
{
print("There are no significant gene by this method(<0.1)")
}else{
#print("MAF plot started 0001")
#print(length(P))
#print(ncolors)
#palette(rainbow(ncolors))
#palette(gray(seq(.9,0,len = ncolors)))
#print("MAF plot started 0001b")
pdf(paste("GAPIT.", trait,".MAF.pdf" ,sep = ""), width = 5,height=5)
par(mar = c(5,6,5,3))
theColor=heat.colors(ncolors, alpha = 1)
palette(rev(theColor))
plot(MAF,LP,type="p",lty = 1,lwd=2,col=LPC,xlab="MAF",ylab =expression(Probability~~-log[10](italic(p))),main = trait, cex.axis=1.1, cex.lab=1.3)
#for(i in 2:nc){
#lines(power[,i]~FDR, lwd=2,type="o",pch=i,col=i)
#}
#legend("bottomright", colnames(power), pch = c(1:nc), lty = c(1,2),col=c(1:nc))
palette("default") # reset back to the default
dev.off()
}
} #GAPIT.MAF ends here
#=============================================================================================
`GAPIT.Main` <-
function(Y,G=NULL,GD=NULL,GM=NULL,KI=NULL,Z=NULL,CV=NULL,CV.Inheritance=NULL,SNP.P3D=TRUE,GP=NULL,GK=NULL,
group.from=1000000 ,group.to=1,group.by=10,kinship.cluster="average", kinship.group='Mean',kinship.algorithm=NULL,DPP=50000,
ngrid = 100, llin = -10, ulim = 10, esp = 1e-10,GAPIT3.output=TRUE,
file.path=NULL,file.from=NULL, file.to=NULL, file.total=NULL, file.fragment = 512, file.G=NULL, file.Ext.G=NULL,file.GD=NULL, file.GM=NULL, file.Ext.GD=NULL,file.Ext.GM=NULL,
SNP.MAF=0,FDR.Rate=1,SNP.FDR=1,SNP.effect="Add",SNP.impute="Middle",PCA.total=0, GAPIT.Version=GAPIT.Version,
name.of.trait, GT = NULL, SNP.fraction = 1, seed = 123, BINS = 20,SNP.test=TRUE,SNP.robust="FaST",
LD.chromosome=NULL,LD.location=NULL,LD.range=NULL,model=model,
bin.from=10000,bin.to=5000000,bin.by=1000,inclosure.from=10,inclosure.to=1000,inclosure.by=10,
SNP.permutation=FALSE,SNP.CV=NULL,NJtree.group=NJtree.group,NJtree.type=NJtree.type,plot.bin=plot.bin,
genoFormat=NULL,hasGenotype=NULL,byFile=NULL,fullGD=NULL,PC=NULL,GI=NULL, Timmer = NULL, Memory = NULL,
sangwich.top=NULL,sangwich.bottom=NULL,QC=TRUE,GTindex=NULL,LD=0.05,
file.output=TRUE,cutOff=0.05, Model.selection = FALSE, Create.indicator = FALSE,
QTN=NULL, QTN.round=1,QTN.limit=0, QTN.update=TRUE, QTN.method="Penalty", Major.allele.zero = FALSE,
QTN.position=NULL,SUPER_GD=NULL,SUPER_GS=SUPER_GS,plot.style="Beach",CG=CG,chor_taxa=chor_taxa){
#Object: To perform GWAS and GPS (Genomic Prediction or Selection)
#Output: GWAS table (text file), QQ plot (PDF), Manhattan plot (PDF), genomic prediction (text file), and
# genetic and residual variance components
#Authors: Zhiwu Zhang
# Last update: Oct 23, 2015 by Jiabo Wang add REML threshold and SUPER GD KI
##############################################################################################
#Initial p3d and h2.opt temporaryly
h2.opt=NULL
p3d=list(
ps=NULL,
REMLs=NULL,
stats=NULL,
effect.est=NULL,
rsquare_base=NULL,
rsquare=NULL,
dfs=NULL,
df=NULL,
tvalue=NULL,
stderr=NULL,
maf=NULL,
nobs=NULL,
Timmer=NULL,
Memory=NULL,
vgs=NULL,
ves=NULL,
BLUP=NULL,
BLUP_Plus_Mean=NULL,
PEV=NULL,
BLUE=NULL,
logLM=NULL,
effect.snp=NULL,
effect.cv=NULL
)
if (SUPER_GS)
{
Compression=NULL
kinship.optimum=NULL
kinship=NULL
PC=PC
REMLs=NULL
GWAS=NULL
QTN=NULL
Timmer=GAPIT.Timmer(Infor="GAPIT.SUPER.GS")
Memory=GAPIT.Memory(Infor="GAPIT.SUPER.GS")
#print(model)
SUPER_GS_GAPIT=GAPIT.SUPER.GS(Y=Y,G=G,GD=GD,GM=GM,KI=KI,Z=Z,CV=CV,GK=GK,kinship.algorithm=kinship.algorithm,
bin.from=bin.from,bin.to=bin.to,bin.by=bin.by,inclosure.from=inclosure.from,inclosure.to=inclosure.to,inclosure.by=inclosure.by,
group.from=group.from,group.to=group.to,group.by=group.by,kinship.cluster=kinship.cluster,kinship.group=kinship.group,name.of.trait=traitname,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF= SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,PCA.total=PCA.total,GAPIT.Version=GAPIT.Version,
GT=GT, SNP.fraction = SNP.fraction, seed = seed, BINS = BINS,SNP.test=SNP.test,DPP=DPP, SNP.permutation=SNP.permutation,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,SNP.CV=SNP.CV,SNP.robust=SNP.robust,model=model,
genoFormat=genoFormat,hasGenotype=hasGenotype,byFile=byFile,fullGD=fullGD,PC=PC,GI=GI,Timmer = Timmer, Memory = Memory,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,QC=QC,GTindex=GTindex,LD=LD,file.output=file.output,cutOff=cutOff
)
print("SUPER_GS_GAPIT FUNCTION DONE")
return (list(Compression=SUPER_GS_GAPIT$Compression,kinship.optimum=SUPER_GS_GAPIT$SUPER_kinship,kinship=SUPER_GS_GAPIT$kinship, PC=SUPER_GS_GAPIT$PC,GWAS=GWAS, GPS=SUPER_GS_GAPIT$GPS,Pred=SUPER_GS_GAPIT$Pred,Timmer=Timmer,Memory=Memory,SUPER_GD=SUPER_GS_GAPIT$SUPER_GD,GWAS=NULL,QTN=NULL))
}else{
#print("@@@@@@@")
#print(group.from)
#Handler of SNP.test=F
#Iniciate with two by seven NA matrix
#The seventh is for p values of SNP
DTS=rbind(rep(NA,7),rep(NA,7) )
#End imediatly in one of these situtiona
shortcut=FALSE
LL.save=1e10
#In case of null Y and null GP, sent back genotype only
thisY=Y[,2]
thisY=thisY[!is.na(thisY)]
if(length(thisY) <3){
shortcut=TRUE
}else{
if(var(thisY) ==0) shortcut=TRUE
}
if(shortcut){
print(paste("Y is empty. No GWAS/GS performed for ",name.of.trait,sep=""))
return (list(compression=NULL,kinship.optimum=NULL, kinship=KI,PC=PC,GWAS=NULL, GPS=NULL,Pred=NULL, REMLs=NULL,Timmer=Timmer,Memory=Memory,h2=NULL))
}
#QC
print("------------Examining data (QC)------------------------------------------")
if(is.null(Y)) stop ("GAPIT says: Phenotypes must exist.")
if(is.null(KI)&missing(GD) & kinship.algorithm!="SUPER") stop ("GAPIT says: Kinship is required. As genotype is not provided, kinship can not be created.")
#When GT and GD are missing, force to have fake ones (creating them from Y),GI is not required in this case
if(is.null(GD) & is.null(GT)) {
GT=as.matrix(Y[,1])
GD=matrix(1,nrow(Y),1)
GI=as.data.frame(matrix(0,1,3) )
colnames(GI)=c("SNP","Chromosome","Position")
}
if(is.null(GT)) {
GT=as.character(Y[,1])
}
#print("@@@@@@@@")
#print(GD)
#merge CV with PC: Put CV infront of PC
if(PCA.total>0&!is.null(CV))CV=GAPIT.CVMergePC(CV,PC)
if(PCA.total>0&is.null(CV))CV=PC
#for GS merge CV with GD name
if (is.null(CV))
{my_allCV=CV
}else{
taxa_GD=rownames(GD)
my_allCV=CV[order(CV[,1]),]
my_allCV=my_allCV[my_allCV[,1]%in%taxa_GD,]
#print(dim(my_allCV))
}
#Handler of CV.Inheritance
if(is.null(CV) & !is.null(CV.Inheritance)){
stop ("GAPIT says: CV.Inheritance is more than avaiable.")
}
if(!is.null(CV)& !is.null(CV.Inheritance)){
if(CV.Inheritance>(ncol(CV)-1)) stop ("GAPIT says: CV.Inheritance is more than avaiable.")
}
#Create Z as identity matrix from Y if it is not provided
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & is.null(Z)){
taxa=as.character(Y[,1]) #this part will make GS without CV not present all prediction
Z=as.data.frame(diag(1,nrow(Y)))
#taxa=as.character(KI[,1])
#Z=as.data.frame(diag(1,nrow(KI)))
Z=rbind(taxa,Z)
taxa=c('Taxa',as.character(taxa))
Z=cbind(taxa,Z)
}
ZI=Z
#Add the part of non proportion in Z matrix
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & !is.null(Z))
{
if(nrow(Z)-1<nrow(Y)) Z=GAPIT.ZmatrixFormation(Z=Z,Y=Y)
}
#Create CV with all 1's if it is not provided
noCV=FALSE
if(is.null(CV)){
noCV=TRUE
CV=Y[,1:2]
CV[,2]=1
colnames(CV)=c("taxa","overall")
}
#Remove duplicat and integragation of data
print("QC is in process...")
CVI <- CV
# print(dim(Z))
if(QC)
{
qc <- GAPIT.QC(Y=Y,KI=KI, GT=GT,CV=CV,Z=Z,GK=GK)
GTindex=qc$GTindex
Y=qc$Y
KI=qc$KI
CV=qc$CV
Z=qc$Z
GK=qc$GK
if(noCV)CVI=qc$CV #this part will make GS without CV not present all prediction
my_taxa=as.character(KI[,1])
}
#print(GTindex)
#print(dim(KI))
#Output phenotype
colnames(Y)=c("Taxa",name.of.trait)
if(file.output)
{try(write.table(Y, paste("GAPIT.", name.of.trait,".phenotype.csv" ,sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE))
}
#TDP
if(kinship.algorithm=="None" )
{
if(min(CV[,2])==max(CV[,2])) CV=NULL
theTDP=GAPIT.TDP(Y=Y,CV=CV,SNP=as.data.frame(cbind(GT[GTindex],as.matrix(as.data.frame(GD[GTindex,])))),
QTN=QTN, Round=QTN.round,QTN.limit=QTN.limit, QTN.update=QTN.update, Method=QTN.method)
#print(dim(GM))
#print(length(theTDP$p))
theGWAS=cbind(GM,theTDP$p,NA,NA,NA)
return (list(Compression=NULL,kinship.optimum=NULL, kinship=NULL,PC=NULL,GWAS=theGWAS, GPS=NULL,Pred=NULL,REMLs=NULL,QTN=theTDP$QTN,Timmer=Timmer,Memory=Memory,h2= NULL))
}
rm(qc)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="QC")
Memory=GAPIT.Memory(Memory=Memory,Infor="QC")
#Get indicator of sangwich top and bottom
byPass.top=FALSE
byPass=FALSE
NOBLUP=FALSE
if(group.from<2&group.to<2) NOBLUP=TRUE
#if(!is.null(sangwich.bottom)) byPass=((sangwich.bottom=="FaST" | sangwich.bottom=="SUPER" | sangwich.bottom=="DC" )& is.null(GP) )
if(!is.null(sangwich.top)) byPass.top=((sangwich.top=="FaST" | sangwich.top=="SUPER" | sangwich.top=="DC" ) )
if(!is.null(sangwich.bottom)) byPass=((sangwich.bottom=="FaST" | sangwich.bottom=="SUPER" | sangwich.bottom=="DC" ) )
print("Try to group from and to were set to 1")
if(byPass){
print("group from and to were set to 1")
group.from=1
group.to=1
}
print("------------Examining data (QC) done-------------------------------------")
#Sagnwich top bun: To gep GP if it is not provided
if(!is.null(sangwich.top) & is.null(GP))
{
print("-------------------Sandwich top bun-----------------------------------")
#print(dim(GD))
#print(GD[1:5,1:5])
#Create GK if not provided
if(is.null(GK)){
# set.seed(1)
nY=floor(nrow(Y)*.9)
nG=ncol(GD)
if(nG>nY){snpsam=sample(1:nG,nY)}else{snpsam=1:nG}
GK=GD[GTindex,snpsam]
SNPVar=apply(as.matrix(GK),2,var)
GK=GK[,SNPVar>0]
GK=cbind(as.data.frame(GT[GTindex]),as.data.frame(GK)) #add taxa
}
#myGD=cbind(as.data.frame(GT),as.data.frame(GD))
file.output.temp=file.output
file.output=FALSE
#print(sangwich.top)
GP=GAPIT.Bread(Y=Y,CV=CV,Z=Z,KI=KI,GK=GK,GD=cbind(as.data.frame(GT),as.data.frame(GD)),GM=GI,method=sangwich.top,GTindex=GTindex,LD=LD,file.output=file.output)$GWAS
file.output=file.output.temp
GK=NULL
print("-------------------Sagnwich top bun: done-----------------------------")
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="SagnwichTop")
Memory=GAPIT.Memory(Memory=Memory,Infor="SagnwichTop")
#Sandwich burger and dressing
print("-------------------Sandwich burger and dressing------------------------")
#Handler of group boundry
if(group.from>group.to) stop("GAPIT says: group.to should be larger than group.from. Please correct them!")
if(is.null(CV) | (!is.null(CV) & group.to<(ncol(CV)+1))) {
#The minimum of group is 1 + number of columns in CV
group.from=1
group.to=1
warning("The upper bound of groups (group.to) is not sufficient. both boundries were set to a and GLM is performed!")
}
if(!is.null(CV)& group.from<1) {
group.from=1 #minimum of group is number of columns in CV
warning("The lower bound of groups should be 1 at least. It was set to 1!")
}
nk=1000000000
if(!is.null(KI)) nk=min(nk,nrow(KI))
if(!is.null(GK)) nk=min(nk,nrow(GK))
if(!is.null(KI))
{
if(group.to>nk) {
#group.to=min(nrow(KI),length(GTindex)) #maximum of group is number of rows in KI
group.to=nk #maximum of group is number of rows in KI
warning("The upper bound of groups is too high. It was set to the size of kinship!")
}
if(group.from>nk){
group.from=nk
warning("The lower bound of groups is too high. It was set to the size of kinship!")
}
}
if(!is.null(CV)){
if(group.to<=ncol(CV)+1) {
#The minimum of group is number of columns in CV
#group.from=ncol(CV)+2
#group.to=ncol(CV)+2
warning("The upper bound of groups (group.to) is not sufficient. both boundries were set to their minimum and GLM is performed!")
}
}
#bin.fold=ceiling(log2(bin.to/bin.from))
#bin.seq=0:bin.fold
#bin.level=bin.from*2^bin.seq
#Set upper bound for inclosure.to
if(inclosure.to>nrow(Y))inclosure.to=nrow(Y)-1
#set inclosure loop levels
bin.level=seq(bin.from,bin.to,by=bin.by)
inclosure=seq(inclosure.from,inclosure.to,by=inclosure.by)
#Optimization for group number, cluster algorithm and kinship type
GROUP=seq(group.to,group.from,by=-group.by)#The reverse order is to make sure to include full model
if(missing("kinship.cluster")) kinship.cluster=c("ward", "single", "complete", "average", "mcquitty", "median", "centroid")
if(missing("kinship.group")) kinship.group=c("Mean", "Max", "Min", "Median")
numSetting=length(GROUP)*length(kinship.cluster)*length(kinship.group)*length(bin.level)*length(inclosure)
#Reform Y, GD and CV into EMMA format
ys=as.matrix(Y[,2])
X0=as.matrix(CV[,-1])
CV.taxa=CVI[,1]
#print(length(ys))
#Initial
count=0
Compression=matrix(,numSetting,6)
colnames(Compression)=c("Type","Cluster","Group","REML","VA","VE")
#add indicator of overall mean
if(min(X0[,1])!=max(X0[,1])) X0 <- cbind(1, X0) #do not add overall mean if X0 has it already at first column
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="DataProcessing")
Memory=GAPIT.Memory(Memory=Memory,Infor="DataProcessing")
print("-------------------------Iteration in process--------------------------")
print(paste("Total iterations: ",numSetting,sep=""))
#Loop to optimize cluster algorithm, group number and kinship type
for (bin in bin.level){
for (inc in inclosure){
#Grill: update KI if GK or GP is provided
if(!byPass & (!is.null(GK) | !is.null(GP)))
{
print("Grilling KI...")
myGenotype<-GAPIT.Genotype(G=NULL,GD=cbind(as.data.frame(GT),as.data.frame(GD)),GM=GI,KI=NULL,kinship.algorithm=kinship.algorithm,PCA.total=0,SNP.fraction=SNP.fraction,SNP.test=SNP.test,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,
file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF=SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,kinship.cluster=kinship.cluster,NJtree.group=NJtree.group,NJtree.type=NJtree.type,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,
GP=GP,GK=GK,bin.size=bin,inclosure.size=inc,SNP.CV=SNP.CV,
Timmer = Timmer, Memory = Memory,GTindex=GTindex,sangwich.top=NULL,sangwich.bottom=sangwich.bottom,
file.output=file.output, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=myGenotype$Timmer
Memory=myGenotype$Memory
KI=myGenotype$KI
#update group set by new KI
nk=nrow(KI)
GROUP=GROUP[GROUP<=nk]
}
for (ca in kinship.cluster){
for (group in GROUP){
for (kt in kinship.group){
#Do not screen SNP unless existing genotype and one combination
if(numSetting==1 & hasGenotype){
optOnly=FALSE
}else{
optOnly=TRUE
}
if(!SNP.test) optOnly=TRUE
if(optOnly | Model.selection){
colInclude=1
optOnly = TRUE
}else{
colInclude=c(1:ncol(GD))
}
if(!optOnly) {print("Compressing and Genome screening..." )}
count=count+1
#Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 1")
#Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 1")
if(!byPass)
{
if(count==1)print("-------Mixed model with Kinship-----------------------------")
if(group<ncol(X0)+1) group=1 # the emma function (emma.delta.REML.dLL.w.Z) does not allow K has dim less then CV. turn to GLM (group=1)
cp <- GAPIT.Compress(KI=KI,kinship.cluster=ca,kinship.group=kt,GN=group,Timmer=Timmer,Memory=Memory)
Timmer=cp$Timmer
Memory=cp$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_cp")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2_cp")
#print("BK...")
bk <- GAPIT.Block(Z=Z,GA=cp$GA,KG=cp$KG)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_bk")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 bk")
#print("ZC...")
zc <- GAPIT.ZmatrixCompress(Z=Z,GAU =bk$GA)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_zc")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 zc")
#print("wraping...")
#Reform KW and Z into EMMA format
zrow=nrow(zc$Z)
zcol=ncol(zc$Z)-1
#Z1=matrix(as.numeric(as.matrix(zc$Z[,-1])),nrow=zrow,ncol=zcol)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Prio PreP3D")
Memory=GAPIT.Memory(Memory=Memory,Infor="Prio PreP3D")
#Evaluating maximum likelohood
#print("Calling EMMAxP3D...")
#print("It made it to here")
#print("The dimension of xs is:")
#print("The value of SNP.impute is")
#print(SNP.impute)
#write.table(zc$Z, "Z.csv", quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#print(dim(as.matrix(as.data.frame(GD[GTindex,colInclude]))))
#print("!!!!!!!!!!!!")
#print(length(ys))
#print(GTindex)
#print(dim(GD))
#print(dim(as.matrix(as.data.frame(GD[GTindex,colInclude]))))
#print(dim(GI))
p3d <- GAPIT.EMMAxP3D(ys=ys,xs=as.matrix(as.data.frame(GD[GTindex,colInclude])),K = as.matrix(bk$KW) ,Z=matrix(as.numeric(as.matrix(zc$Z[,-1])),nrow=zrow,ncol=zcol),X0=X0,CVI=CVI,CV.Inheritance=CV.Inheritance,GI=GI,SNP.P3D=SNP.P3D,Timmer=Timmer,Memory=Memory,fullGD=fullGD,
SNP.permutation=SNP.permutation, GP=GP,SNP.fraction=SNP.fraction,
file.path=file.path,file.from=file.from,file.to=file.to,file.total=file.total, file.fragment = file.fragment, byFile=byFile, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
GTindex=GTindex,genoFormat=genoFormat,optOnly=optOnly,SNP.effect=SNP.effect,SNP.impute=SNP.impute,name.of.trait=name.of.trait, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=p3d$Timmer
Memory=p3d$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Post PreP3D")
Memory=GAPIT.Memory(Memory=Memory,Infor="Post PreP3D")
#print("Cluster algorithm, kinship type, groups, VG, Ve and REML:")
print(paste(count, "of",numSetting,"--","Vg=",round(p3d$vgs,4), "VE=",round(p3d$ves,4),"-2LL=",round(p3d$REMLs,2), " Clustering=",ca," Group number=", group ," Group kinship=",kt,sep = " "))
#print(table(GTindex))
#Recoding the optimum KI
if(count==1){
KI.save=KI
LL.save=p3d$REMLs
}else{
if(p3d$REMLs<LL.save){
KI.save=KI
LL.save=p3d$REMLs
}
}
#print(paste("CA is ",ca))
#print(paste("group is ",group))
#print(paste("kt is ",kt))
#recording Compression profile on array
Compression[count,1]=kt
Compression[count,2]=ca
Compression[count,3]=group
Compression[count,4]=p3d$REMLs
Compression[count,5]=p3d$vgs
Compression[count,6]=p3d$ves
#print("result saved")
}else{# end of if(!byPass)
#Set QTNs
if(count==1)print("-------The burger is SNP-----------------------------------")
#bin.size=bin
#inclosure.size=inc
#@@@This section is not useful
if(!is.null(GP))
{
#print("Being specific...")
myGenotype<-GAPIT.Genotype(G=NULL,GD=NULL,GM=GI,KI=NULL,kinship.algorithm="SUPER",PCA.total=0,SNP.fraction=SNP.fraction,SNP.test=SNP.test,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,
file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF=SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,kinship.cluster=kinship.cluster,#NJtree.group=NJtree.group,NJtree.type=NJtree.type,
GP=GP,GK=NULL,bin.size=bin,inclosure.size=inc,SNP.CV=SNP.CV,GTindex=GTindex,sangwich.top=NULL,sangwich.bottom=sangwich.bottom,
Timmer = Timmer, Memory = Memory,file.output=file.output, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=myGenotype$Timmer
Memory=myGenotype$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype for burger")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype for burger")
print(paste("bin---",bin,"---inc---",inc,sep=""))
GK=GD[GTindex,myGenotype$SNP.QTN]
SUPER_GD=GD[,myGenotype$SNP.QTN]
SNPVar=apply(as.matrix(GK),2,var)
GK=GK[,SNPVar>0]
SUPER_GD=SUPER_GD[,SNPVar>0]
GK=cbind(as.data.frame(GT[GTindex]),as.data.frame(GK)) #add taxa
SUPER_GD=cbind(as.data.frame(GT),as.data.frame(SUPER_GD)) #add taxa
#GP=NULL
}# end of if(is.null(GK))
if(!is.null(GK) & numSetting>1)
{
print("-------Calculating likelihood-----------------------------------")
# myBurger=GAPIT.Burger(Y=Y,CV=CV,GK=GK)
myBurger=GAPIT.Burger(Y=Y,CV=NULL,GK=GK) #########modified by Jiabo Wang
myREML=myBurger$REMLs
myVG=myBurger$vg
myVE=myBurger$ve
}else{
myREML=NA
myVG=NA
myVE=NA
}
#Recoding the optimum GK
if(count==1){
GK.save=GK
LL.save=myREML
SUPER_optimum_GD=SUPER_GD ########### get SUPER GD
}else{
if(myREML<LL.save){
GK.save=GK
LL.save=myREML
SUPER_optimum_GD=SUPER_GD ########### get SUPER GD
}
}
#Put to storage
Compression[count,1]=1
Compression[count,2]=bin
Compression[count,3]=inc
Compression[count,4]=myREML
Compression[count,5]=myVG
Compression[count,6]=myVG
print(Compression[count,])
#print("---------------SUPER 2nd stage: calculating LL ------------------------")
} # end of if(byPass)
}#end of for (ca in kinship.cluster)
#Skip the rest group in case group 1 is finished
if(group==1) break #To skip the rest group interations
}#end of for (group in GROUP)
}#end of for (kt in kinship.group)
}#end of for (inc in inclosure)
}#end of for (bin in bin.level)
if(Model.selection == TRUE){
print("------------------------Model selection for optimal number of PCs and Covariates-------------------------------------------------")
#update KI with the best likelihood
KI=KI.save
if(numSetting>1){
Compression=Compression[order(as.numeric(Compression[,4]),decreasing = FALSE),] #sort on REML
kt=Compression[1,1]
ca=Compression[1,2]
group=Compression[1,3]
}
cp <- GAPIT.Compress(KI=KI,kinship.cluster=ca,kinship.group=kt,GN=group,Timmer=Timmer,Memory=Memory)
Timmer=cp$Timmer
Memory=cp$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_cp")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2_cp")
bk <- GAPIT.Block(Z=Z,GA=cp$GA,KG=cp$KG)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_bk")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 bk")
zc <- GAPIT.ZmatrixCompress(Z=Z,GAU =bk$GA)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_zc")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 zc")
z0=as.matrix(zc$Z[,-1])
Z1=matrix(as.numeric(z0),nrow=nrow(z0),ncol=ncol(z0))
BIC <- rep(NA,ncol(X0))
LogLike <- rep(NA, ncol(X0))
for(i in 1:ncol(X0)){#1 because the first column of X0 is the intercept
X0.test <- as.matrix(X0[,1:i])
#print("The dim of bk$KW is ")
#print(dim(bk$KW))
#print(dim(X0.test))
#print(dim(CVI))
p3d <- GAPIT.EMMAxP3D(ys=ys,xs=as.matrix(as.data.frame(GD[,1])),K = as.matrix(bk$KW) ,Z=Z1,X0=X0.test,CVI=CVI,CV.Inheritance=CV.Inheritance,GI=GI,SNP.P3D=SNP.P3D,Timmer=Timmer,Memory=Memory,fullGD=fullGD,
SNP.permutation=SNP.permutation, GP=GP,
file.path=file.path,file.from=file.from,file.to=file.to,file.total=file.total, file.fragment = file.fragment, byFile=byFile, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
GTindex=GTindex,genoFormat=genoFormat,optOnly=TRUE,SNP.effect=SNP.effect,SNP.impute=SNP.impute,name.of.trait=name.of.trait, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
k.num.param <- 2+i
#k is (i-1) because we have the following parameters in the likelihood function:
# intercept
# (i-1) covariates
# sigma_g
# delta
#print(paste("The value of round(p3d$REMLs,5) is ", round(p3d$REMLs,5), sep = ""))
#print(paste("The value of log(GTindex) is ", log(GTindex), sep = ""))
#print(paste("The value of 0.5*k.num.param*log(GTindex) is ", 0.5*k.num.param*log(nrow(Z1)), sep = ""))
LogLike[i] <- p3d$logLM
BIC[i] <- p3d$logLM -(0.5*k.num.param*log(nrow(Z1)))
#print("The value of k.num.param is: ")
#print(k.num.param)
#print(paste("The value of nrow(Z1) is ", nrow(Z1), sep = ""))
}
Optimum.from.BIC <- which(BIC == max(BIC))
print(paste("-----------------------The optimal number of PCs/covariates is ", (Optimum.from.BIC-1)," -------------------------", sep = ""))
BIC.Vector <- cbind(as.matrix(rep(0:(ncol(X0)-1))), as.matrix(BIC), as.matrix(LogLike))
#print(seq(0:ncol(X0)))
#print(BIC.Vector)
colnames(BIC.Vector) <- c("Number of PCs/Covariates", "BIC (larger is better) - Schwarz 1978", "log Likelihood Function Value")
write.table(BIC.Vector, paste("GAPIT.", name.of.trait, ".BIC.Model.Selection.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#print(BIC.Vector)
X0 <- X0[,1:(Optimum.from.BIC)]
if(Optimum.from.BIC == 1){
X0 <- as.matrix(X0)
}
print("The dimension of X0 after model selection is:")
print(dim(X0))
print("The head of X0 after model selection is")
print(head(X0))
} # where does it start: 522
print("---------------------Sandwich bottom bun-------------------------------")
print("Compression")
print(Compression)
#Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Compression")
#Memory=GAPIT.Memory(Memory=Memory,Infor="Copmression")
if(numSetting==1)
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GWAS")
Memory=GAPIT.Memory(Memory=Memory,Infor="GWAS")
}
#Perform GWAS with the optimum setting
#This section is omited if there is only one setting
if((numSetting>1)| (!is.null(sangwich.bottom)&!byPass) | Model.selection) {
print("Genomic screening..." )
optOnly=FALSE #set default to false and change it to TRUE in these situations:
if(!hasGenotype) optOnly=TRUE
if(!SNP.test) optOnly=TRUE
if(optOnly){
colInclude=1
}else{
colInclude=c(1:ncol(GD))
}
if(numSetting>1){
#Find the best ca,kt and group
print(paste(as.numeric(Compression[1,4]))) ###added by Jiabo Wang 2015.7.20
print(paste(min(as.numeric(Compression[,4]),rm.na=TRUE)))
adjust_value=as.numeric(Compression[1,4])-min(as.numeric(Compression[,4]),rm.na=TRUE)
nocompress_value=as.numeric(Compression[1,4])
REML_storage=as.numeric(Compression[,4])
adjust_mean=mean(as.numeric(Compression[,4]),rm.na=TRUE)
threshold=adjust_mean*0.1
if(adjust_value<3|nocompress_value<0) ###added by Jiabo Wang 2015.7.20
{
kt=Compression[1,1]
ca=Compression[1,2]
group=Compression[1,3]
print(paste("Optimum: ",Compression[1,2],Compression[1,1],Compression[1,3],Compression[1,5], Compression[1,6],Compression[1,4] ,sep = " "))
}else{
Compression=Compression[order(as.numeric(Compression[,4]),decreasing = FALSE),] #sort on REML
kt=Compression[1,1]
ca=Compression[1,2]
group=Compression[1,3]
print(paste("Optimum: ",Compression[1,2],Compression[1,1],Compression[1,3],Compression[1,5], Compression[1,6],Compression[1,4] ,sep = " "))
}
}#end if(numSetting>1)
print("-------------- Sandwich bottom ------------------------")
if(!byPass)
{
print("-------------- Sandwich bottom with raw burger------------------------")
if(Model.selection == FALSE){
#update KI with the best likelihood
if(is.null(sangwich.bottom)) KI=KI.save
cp <- GAPIT.Compress(KI=KI,kinship.cluster=ca,kinship.group=kt,GN=group,Timmer=Timmer,Memory=Memory)
Timmer=cp$Timmer
Memory=cp$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_cp")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2_cp")
bk <- GAPIT.Block(Z=Z,GA=cp$GA,KG=cp$KG)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_bk")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 bk")
zc <- GAPIT.ZmatrixCompress(Z=Z,GAU =bk$GA)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_zc")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 zc")
#Reform KW and Z into EMMA format
z0=as.matrix(zc$Z[,-1])
Z1=matrix(as.numeric(z0),nrow=nrow(z0),ncol=ncol(z0))
}
print("--------------EMMAxP3D with the optimum setting-----------------------")
#print(dim(ys))
#print(dim(as.matrix(as.data.frame(GD[GTindex,colInclude]))))
p3d <- GAPIT.EMMAxP3D(ys=ys,xs=as.matrix(as.data.frame(GD[GTindex,colInclude])) ,K = as.matrix(bk$KW) ,Z=Z1,X0=as.matrix(X0),CVI=CVI, CV.Inheritance=CV.Inheritance,GI=GI,SNP.P3D=SNP.P3D,Timmer=Timmer,Memory=Memory,fullGD=fullGD,
SNP.permutation=SNP.permutation, GP=GP,
file.path=file.path,file.from=file.from,file.to=file.to,file.total=file.total, file.fragment = file.fragment, byFile=byFile, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
GTindex=GTindex,genoFormat=genoFormat,optOnly=optOnly,SNP.effect=SNP.effect,SNP.impute=SNP.impute,name.of.trait=name.of.trait, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GWAS")
Memory=GAPIT.Memory(Memory=Memory,Infor="GWAS")
print("--------------EMMAxP3D with the optimum setting done------------------")
}#end of if(!byPass)
}#end of if(numSetting>1 & hasGenotype & !SNP.test)
#print("Screening wiht the optimum setting done")
if(byPass)
{
print("---------------Sandwich bottom with grilled burger---------------------")
print("---------------Sandwich bottom: reload bins ---------------------------")
#SUPER: Final screening
GK=GK.save
myBread=GAPIT.Bread(Y=Y,CV=CV,Z=Z,GK=GK,GD=cbind(as.data.frame(GT),as.data.frame(GD)),GM=GI,method=sangwich.bottom,GTindex=GTindex,LD=LD,file.output=file.output)
print("SUPER saving results...")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GWAS")
Memory=GAPIT.Memory(Memory=Memory,Infor="GWAS")
} #end of if(byPass)
print("--------------------Final results presentations------------------------")
#Plotting optimum group kinship
if(!byPass)
{
if(length(bk$KW)>1 &length(bk$KW)<length(KI) & length(bk$KW)<1000 &GAPIT3.output){
pdf(paste("GAPIT.",name.of.trait,".Kin.Optimum.pdf",sep=""), width = 12, height = 12)
par(mar = c(25,25,25,25))
heatmap.2(as.matrix(bk$KW), cexRow =.2, cexCol = 0.2, col=rev(heat.colors(256)), scale="none", symkey=FALSE, trace="none")
dev.off()
}
}
#Merge GWAS resultss from files to update ps,maf and nobs in p3d
if(byFile&!fullGD)
{
print("Loading GWAS results from file...")
for (file in file.from:file.to)
{
#Initicalization
frag=1
numSNP=file.fragment
while(numSNP==file.fragment) { #this is problematic if the read end at the last line
#Initicalization GI to detect reading empty line
#theGI=NULL
#theP=NULL
#theMAF=NULL
#thenobs=NULL
#reload results from files
print(paste("Current file ",file,"Fragment: ",frag))
theGI <- try(read.table(paste("GAPIT.TMP.GI.",name.of.trait,file,".",frag,".txt",sep=""), head = TRUE) ,silent=TRUE)
theP <- try(read.table(paste("GAPIT.TMP.ps.",name.of.trait,file,".",frag,".txt",sep=""), head = FALSE) ,silent=TRUE)
theMAF <- try(read.table(paste("GAPIT.TMP.maf.",name.of.trait,file,".",frag,".txt",sep=""), head = FALSE),silent=TRUE)
thenobs <- try(read.table(paste("GAPIT.TMP.nobs.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
thersquare_base <- try(read.table(paste("GAPIT.TMP.rsquare.base.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
thersquare <- try(read.table(paste("GAPIT.TMP.rsquare.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
thedf <- try(read.table(paste("GAPIT.TMP.df.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
thetvalue <- try(read.table(paste("GAPIT.TMP.tvalue.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
thestderr <- try(read.table(paste("GAPIT.TMP.stderr.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
theeffect.est <- try(read.table(paste("GAPIT.TMP.effect.est.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
if(inherits(theGI, "try-error")) {
#if(nrow(theGI)<1){
numSNP=0
#print("This fragment is empty.")
}else{
#print("Records loaded for this fragment.")
numSNP=nrow(theGI)
colnames(theP)="P"
colnames(theMAF )="MAF"
colnames(thenobs )="nobs"
colnames(thersquare_base) = "Base.Model.R.square"
colnames(thersquare) = "Model.R.square"
colnames(thedf) = "Model.DF"
colnames(thetvalue) = "Model.tvalue"
colnames(thestderr) = "Model.stderr"
colnames(theeffect.est) = "Effect.Est"
colnames(theGI) = colnames(GI)
#Merge results
if(file==file.from & frag==1){
GI=theGI
#print(dim(GI))
allP=theP
#print(head(theP))
allMAF=theMAF
allnobs=thenobs
allrsquare_base=thersquare_base
allrsquare=thersquare
alldf=thedf
alltvalue=thetvalue
allstderr=thestderr
alleffect.est=theeffect.est
}else{
allP=as.data.frame(rbind(as.matrix(allP),as.matrix(theP)) )
allMAF=as.data.frame(rbind(as.matrix(allMAF),as.matrix(theMAF)) )
allnobs=as.data.frame(rbind(as.matrix(allnobs),as.matrix(thenobs)))
allrsquare_base=as.data.frame(rbind(as.matrix(allrsquare_base),as.matrix(thersquare_base)))
allrsquare=as.data.frame(rbind(as.matrix(allrsquare),as.matrix(thersquare)))
alldf=as.data.frame(rbind(as.matrix(alldf),as.matrix(thedf)))
alltvalue=as.data.frame(rbind(as.matrix(alltvalue),as.matrix(thetvalue)))
allstderr=as.data.frame(rbind(as.matrix(allstderr),as.matrix(thestderr)))
alleffect.est=as.data.frame(rbind(as.matrix(alleffect.est),as.matrix(theeffect.est)))
#print("!!!!!!!!!!!!!!!")
#print(dim(GI))
#print(dim(theGI))
GI=as.data.frame(rbind(as.matrix(GI),as.matrix(theGI)))
}
}#end of if(inherits(theGI, "try-error")) (else section)
#setup for next fragment
frag=frag+1 #Progress to next fragment
}#end of loop on fragment: while(numSNP==file.fragment)
}#end of loop on file
#update p3d with components from files
p3d$ps=allP
p3d$maf=allMAF
p3d$nobs=allnobs
p3d$rsquare_base=allrsquare_base
p3d$rsquare=allrsquare
p3d$df=alldf
p3d$tvalue=alltvalue
p3d$stderr=allstderr
p3d$effect.est=alleffect.est
#Delete all the GAPIT.TMP files
theFile=paste("GAPIT.TMP.",name.of.trait,".*")
system('cmd /c del "GAPIT.TMP*.*"')
system('cmd /c del "GAPIT.TMP*.*"')
print("GWAS results loaded from all files succesfully!")
} #end of if(byFile)
#--------------------------------------------------------------------------------------------------------------------#
#Final report
print("Generating summary" )
GWAS=NULL
GPS=NULL
rm(zc)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Final")
Memory=GAPIT.Memory(Memory=Memory,Infor="Final")
#genomic prediction
print("Genomic Breeding Values (GBV) ..." )
#print(p3d$BLUP)
gs=NULL
if(!byPass)
{
if(length(bk$KW)>ncol(X0)) {
gs <- GAPIT.GS(KW=bk$KW,KO=bk$KO,KWO=bk$KWO,GAU=bk$GAU,UW=cbind(p3d$BLUP,p3d$PEV))
}
print("Writing GBV and Acc..." )
GPS=NULL
if(length(bk$KW)>ncol(X0)) GPS=gs$BLUP
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GPS")
Memory=GAPIT.Memory(Memory=Memory,Infor="GPS")
#Make heatmap for distribution of BLUP and PEV
print("GBV and accuracy distribution..." )
if(length(bk$KW)>ncol(X0) &file.output) {
GAPIT.GS.Visualization(gsBLUP = gs$BLUP, BINS=BINS,name.of.trait = name.of.trait)
}
#Make a plot Summarzing the Compression Results, if more than one "compression level" has been assessed
print("Compression portfolios..." )
#print(Compression)
if(file.output) GAPIT.Compression.Visualization(Compression = Compression, name.of.trait = name.of.trait)
print("Compression Visualization done")
if(length(Compression)<1){
h2.opt= NULL
}else{
if(length(Compression)<=6) Compression=t(as.matrix(Compression[which(Compression[,4]!="NULL" | Compression[,4]!="NaN"),]))
if(length(Compression)==6) Compression=matrix(Compression,1,6)
if(length(Compression)>6) Compression=Compression[which(Compression[,4]!="NULL" | Compression[,4]!="NaN"),]
Compression.best=Compression[1,]
variance=as.numeric(Compression.best[5:6])
varp=variance/sum(variance)
h2.opt= varp[1]
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Compression.Visualization")
Memory=GAPIT.Memory(Memory=Memory,Infor="Compression.Visualization")
# print("$$$$$")
# print(str(p3d))
ps=p3d$ps
nobs=p3d$nobs
maf=p3d$maf
rsquare_base=p3d$rsquare_base
rsquare=p3d$rsquare
df=p3d$df
tvalue=p3d$tvalue
stderr=p3d$stderr
effect.est=p3d$effect.est
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Extract p3d results")
Memory=GAPIT.Memory(Memory=Memory,Infor="Extract p3d results")
print("p3d objects transfered")
#where does it start: 936
}else{ #byPass
#print("The head of myBread$GWAS is")
#print(head(myBread$GWAS))
GPS=myBread$BLUP
ps=myBread$GWAS[,4]
nobs=myBread$GWAS[,6]
#print(dim(GI))
#print(head())
Bread_index=match(as.character(myBread$GWAS[,1]),as.character(GI[,1]))
#print(GD[1:5,1:5])
Bread_X=GD[,Bread_index]
#print(dim(Bread_X))
maf=apply(Bread_X,2,function(one) abs(1-sum(one)/(2*nrow(Bread_X))))
maf[maf>0.5]=1-maf[maf>0.5]
rsquare_base=rep(NA,length(ps))
rsquare=rep(NA,length(ps))
df=rep(NA,length(nobs))
tvalue=rep(NA,length(nobs))
stderr=rep(NA,length(nobs))
effect.est=rep(NA,length(nobs))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Extract bread results")
Memory=GAPIT.Memory(Memory=Memory,Infor="Extract bread results")
}
print("Merge BLUP and BLUE")
#print(head(ps))
#Merge BLUP and BLUE
Pred=NULL
if((!byPass)&(!Model.selection)){
print("GAPIT before BLUP and BLUE")
#print(dim(p3d$BLUE))
BLUE=data.frame(cbind(data.frame(CV.taxa),data.frame(p3d$BLUE)))
colnames(BLUE)=c("Taxa","BLUE")
#Initial BLUP as BLUe and add additional columns
gs.blup=cbind(BLUE,NA,NA,0,NA)
if(!is.null(gs))gs.blup=gs$BLUP
BB= merge(gs.blup, BLUE, by.x = "Taxa", by.y = "Taxa")
if (is.null(my_allCV)){my_allX=matrix(1,length(my_taxa),1)
}else{
# my_allX=as.matrix(my_allCV[,-1])
my_allX=cbind(1,as.matrix(my_allCV[,-1]))
}
#print(dim(my_allX))
#print(head(my_allX))
#print(dim(BB))
#print(CV.Inheritance)
if(is.null(CV.Inheritance))
{
Prediction=BB[,5]+BB[,7]
Pred_Heritable=Prediction
}
if(!is.null(CV.Inheritance))
{
#inher_CV=my_allX[,1:(1+CV.Inheritance)]
#beta.Inheritance=p3d$effect.cv[1:(1+CV.Inheritance)]
#print(beta.Inheritance)
#if(length(beta)==1)CV=X
all_BLUE=try(my_allX%*%p3d$effect.cv,silent=T)
if(inherits(BLUE, "try-error")) all_BLUE = NA
Pred_Heritable=BB[,5]+BB[,7]
Prediction=BB[,5]+all_BLUE
}
#print("@@@@@@@@@@")
#print(dim(CVI))
#print(BB)
#CV.Inheritance
#Pred_Heritable=p3d$effect.cv[CV.Inheritance]%*%CVI[CV.Inheritance]+BB[,7]
Pred=data.frame(cbind(BB,data.frame(Prediction)),data.frame(Pred_Heritable))
if(noCV)
{
if(NOBLUP)
{Pred=NA
}else{
BLUE=Pred$BLUE[1]
prediction=as.matrix(GPS$BLUP)+(BLUE)
Pred=cbind(GPS,BLUE,prediction)
colnames(Pred)=c("Taxa","Group","RefInf","ID","BLUP","PEV","BLUE","Prediction")
}#end NOBLUP
}#end noCV
print("GAPIT after BLUP and BLUE")
}
#Export BLUP and PEV
if(!byPass &GAPIT3.output)
{
print("Exporting BLUP and Pred")
#try(write.table(gs$BLUP, paste("GAPIT.", name.of.trait,".BLUP.csv" ,sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE))
try(write.table(Pred, paste("GAPIT.", name.of.trait,".PRED.csv" ,sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE))
}
if(byPass)
{
theK.back=NULL
}else{
theK.back=cp$KG
}
if(byPass)Compression[1,4]=0 #create a fake value to aloow output of SUPER
#Export GWAS results
PWI.Filtered=NULL
if(hasGenotype &SNP.test &!is.na(Compression[1,4])) #require not NA REML
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Extract GWAS start")
Memory=GAPIT.Memory(Memory=Memory,Infor="Extract GWAS start")
#print("Filtering SNPs with MAF..." )
#index=maf>=SNP.MAF
PWI.Filtered=cbind(GI,ps,maf,nobs,rsquare_base,rsquare,effect.est)#[index,]
#print(dim(PWI.Filtered))
colnames(PWI.Filtered)=c("SNP","Chromosome","Position ","P.value", "maf", "nobs", "Rsquare.of.Model.without.SNP","Rsquare.of.Model.with.SNP","effect")
if(!byPass){
if(Create.indicator){
#Add a counter column for GI
GI.counter <- cbind(GI, seq(1:nrow(GI)))
#Turn GI and effect.est into data frames
GI.counter.data.frame <- data.frame(GI.counter)
colnames(GI.counter.data.frame) <- c("X1", "X2", "X3", "X4")
effect.est.data.frame <- data.frame(effect.est)
colnames(effect.est.data.frame) <- c("X1", "X2", "X3")
print(head(GI.counter.data.frame))
print(head(effect.est.data.frame))
#Do a merge statement
GWAS.2 <- merge(GI.counter.data.frame, effect.est.data.frame, by.x = "X4", by.y = "X1")
#Remove the counter column
GWAS.2 <- GWAS.2[,-1]
#Add column names
colnames(GWAS.2) <- c("SNP","Chromosome","Position ", "Genotype", "Allelic Effect Estimate")
}
if(!Create.indicator){
GWAS.2 <- PWI.Filtered[,c(1:3,9)]
colnames(GWAS.2) <- c("SNP","Chromosome","Position ", "Allelic Effect Estimate")
}
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="MAF filtered")
Memory=GAPIT.Memory(Memory=Memory,Infor="MAF filtered")
#print("SNPs filtered with MAF")
if(!is.null(PWI.Filtered))
{
#Run the BH multiple correction procedure of the results
#Create PWIP, which is a table of SNP Names, Chromosome, bp Position, Raw P-values, FDR Adjusted P-values
#print("Calculating FDR..." )
PWIP <- GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure(PWI = PWI.Filtered, FDR.Rate = FDR.Rate, FDR.Procedure = "BH")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Multiple Correction")
Memory=GAPIT.Memory(Memory=Memory,Infor="Multiple Correction")
#QQ plots
#print("QQ plot..." )
if(file.output) GAPIT.QQ(P.values = PWIP$PWIP[,4], name.of.trait = name.of.trait,DPP=DPP)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="QQ plot")
Memory=GAPIT.Memory(Memory=Memory,Infor="QQ plot")
#Manhattan Plots
#print("Manhattan plot (Genomewise)..." )
# if(file.output) GAPIT.Manhattan(GI.MP = PWIP$PWIP[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff)
# if(file.output) GAPIT.Manhattan(GI.MP = PWIP$PWIP[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff,seqQTN=QTN.position) #QTN does not work with sorted P
if(file.output) GAPIT.Manhattan(GI.MP = PWI.Filtered[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff,seqQTN=QTN.position,plot.style=plot.style,plot.bin=plot.bin,chor_taxa=chor_taxa)
#print("Manhattan plot (Chromosomewise)..." )
#if(file.output) GAPIT.Manhattan(GI.MP = PWIP$PWIP[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Chromosomewise",cutOff=cutOff)
if(file.output&SNP.fraction==1) GAPIT.Manhattan(GI.MP = PWI.Filtered[,2:4],GD=GD,CG=CG, name.of.trait = name.of.trait, DPP=DPP, plot.type = "Chromosomewise",cutOff=cutOff,plot.bin=plot.bin,chor_taxa=chor_taxa)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Manhattan plot")
Memory=GAPIT.Memory(Memory=Memory,Infor="Manhattan plot")
#Association Table
#print("Association table..." )
#print(dim(PWIP$PWIP))
#GAPIT.Table(final.table = PWIP$PWIP, name.of.trait = name.of.trait,SNP.FDR=SNP.FDR)
#print(head(PWIP$PWIP))
GWAS=PWIP$PWIP[PWIP$PWIP[,9]<=SNP.FDR,]
#print("Joining tvalue and stderr" )
DTS=cbind(GI,df,tvalue,stderr,effect.est)
colnames(DTS)=c("SNP","Chromosome","Position","DF","t Value","std Error","effect")
#print("Creating ROC table and plot" )
if(file.output) myROC=GAPIT.ROC(t=tvalue,se=stderr,Vp=var(ys),trait=name.of.trait)
#print("ROC table and plot created" )
#MAF plots
#print("MAF plot..." )
if(file.output) myMAF1=GAPIT.MAF(MAF=GWAS[,5],P=GWAS[,4],E=NULL,trait=name.of.trait)
#print(dim(GWAS))
if(file.output){
write.table(GWAS, paste("GAPIT.", name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
write.table(DTS, paste("GAPIT.", name.of.trait, ".Df.tValue.StdErr.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
if(!byPass) write.table(GWAS.2, paste("GAPIT.", name.of.trait, ".Allelic_Effect_Estimates.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}
} #end of if(!is.null(PWI.Filtered))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Extract GWAS end")
Memory=GAPIT.Memory(Memory=Memory,Infor="Extract GWAS end")
} #end of if(hasGenotype )
#Log
if(GAPIT3.output) log=GAPIT.Log(Y=Y,KI=KI,Z=Z,CV=CV,SNP.P3D=SNP.P3D,
group.from = group.from ,group.to =group.to ,group.by = group.by ,kinship.cluster = kinship.cluster, kinship.group= kinship.group,
ngrid = ngrid , llin = llin , ulim = ulim , esp = esp ,name.of.trait = name.of.trait)
#Memory usage
#GAPIT.Memory.Object(name.of.trait=name.of.trait)
#Timming
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Report")
Memory=GAPIT.Memory(Memory=Memory,Infor="Report")
if(file.output){
file=paste("GAPIT.", name.of.trait,".Timming.csv" ,sep = "")
write.table(Timmer, file, quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
file=paste("GAPIT.", name.of.trait,".Memory.Stage.csv" ,sep = "")
write.table(Memory, file, quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}
print(paste(name.of.trait, "has been analyzed successfully!") )
print(paste("The results are saved in the directory of ", getwd()) )
#print("==========================================================================================")
TV<-list()
TV$ps=ps
TV$nobs=nobs
TV$maf=maf
TV$rsquare_base=rsquare_base
TV$rsquare=rsquare
TV$df=df
TV$tvalue=tvalue
TV$stderr=stderr
TV$effect.est=effect.est
#print("!!!!!!!!!!!!!")
#print(head(effect.est))
#print(head(DTS[,7]))
#print(ys)
if(byPass | Model.selection) Pred <- NA
print("before ending GAPIT.Main")
#print(dim(Compression))
return (list(Timmer=Timmer,Compression=Compression,kinship.optimum=theK.back, kinship=KI,PC=PC,GWAS=PWI.Filtered, GPS=GPS,Pred=Pred,REMLs=Compression[count,4],Timmer=Timmer,Memory=Memory,SUPER_GD=SUPER_GD,P=ps,effect.snp=DTS[,7],effect.cv=p3d$effect.cv,h2= h2.opt,TV=TV))
} #end if non-SUPER.GS situation, this is a long if statement, structure needs improvement
}#The function GAPIT.Main ends here
#=============================================================================================
`GAPIT.Manhattan` <-
function(GI.MP = NULL,GD=NULL,name.of.trait = "Trait",plot.type = "Genomewise",
DPP=50000,cutOff=0.01,band=5,seqQTN=NULL,plot.style="Oceanic",CG=NULL,plot.bin=10^9,chor_taxa=NULL){
#Object: Make a Manhattan Plot
#Options for plot.type = "Separate_Graph_for_Each_Chromosome" and "Same_Graph_for_Each_Chromosome"
#Output: A pdf of the Manhattan Plot
#Authors: Alex Lipka, Zhiwu Zhang, Meng Li and Jiabo Wang
# Last update: Oct 10, 2016
#Add r2 between candidata SNP and other markers in on choromosome
##############################################################################################
#print("Manhattan ploting...")
#print(cutOff)
#do nothing if null input
if(is.null(GI.MP)) return
#if(is.null(GD)) return
#print("Dimension of GI.MP")
#print(dim(GI.MP))
#print(head(GI.MP))
#print(tail(GI.MP))
#print(CG)
#seqQTN=c(300,1000,2500)
#Handler of lable paosition only indicated by negatie position
position.only=F
if(!is.null(seqQTN)){
if(seqQTN[1]<0){
seqQTN=-seqQTN
position.only=T
}
}
#if(is.null(GD)) print ("GD is not same dim as GM")
borrowSlot=4
GI.MP[,borrowSlot]=0
GI.MP[,5]=1:(nrow(GI.MP))
GI.MP=matrix(as.numeric(as.matrix(GI.MP) ) ,nrow(GI.MP),ncol(GI.MP))
GI.MP=GI.MP[order(GI.MP[,2]),]
GI.MP=GI.MP[order(GI.MP[,1]),]
# print("@@@@@")
# print(head(GI.MP))
#Inicial as 0
if(!is.null(seqQTN))GI.MP[seqQTN,borrowSlot]=1
if(!is.null(GD))
{ if(ncol(GD)!=nrow(GI.MP))print("GD does not mach GM in Manhattan !!!")
}
#print(ncol(GD))
#print(nrow(GI.MP))
#print(GI.MP)
#print("!!")
#GI.MP[,5]=1:(nrow(GI.MP))
#print(head(GI.MP,20))
#Remove all SNPs that do not have a choromosome, bp position and p value(NA)
GI.MP <- GI.MP[!is.na(GI.MP[,1]),]
GI.MP <- GI.MP[!is.na(GI.MP[,2]),]
if(!is.null(GD)) GD=GD[,!is.na(GI.MP[,3])]
GI.MP <- GI.MP[!is.na(GI.MP[,3]),]
#Retain SNPs that have P values between 0 and 1 (not na etc)
if(!is.null(GD)) GD=GD[,GI.MP[,3]>0]
GI.MP <- GI.MP[GI.MP[,3]>0,]
if(!is.null(GD)) GD=GD[,GI.MP[,3]<=1]
GI.MP <- GI.MP[GI.MP[,3]<=1,]
#Remove chr 0 and 99
GI.MP <- GI.MP[GI.MP[,1]!=0,]
#GI.MP <- GI.MP[GI.MP[,1]!=99,]
#print(dim(GI.MP))
#print("Dimension of GI.MP after QC")
#print(dim(GI.MP))
#print(head(GI.MP))
numMarker=nrow(GI.MP)
#print(numMarker)
bonferroniCutOff=-log10(cutOff/numMarker)
#Replace P the -log10 of the P-values
if(!is.null(GD))
{ if(ncol(GD)!=nrow(GI.MP))
{print("GD does not match GM in Manhattan !!!")
return
}}
#print(ncol(GD))
#print(nrow(GI.MP))
GI.MP[,3] <- -log10(GI.MP[,3])
index_GI=GI.MP[,3]>0
GI.MP <- GI.MP[index_GI,]
if(!is.null(GD)) GD=GD[,index_GI]
GI.MP[,5]=1:(nrow(GI.MP))
y.lim <- ceiling(max(GI.MP[,3]))
chm.to.analyze <- unique(GI.MP[,1])
#print(dim(GI.MP))
#print(dim(GD))
#print("name of chromosomes:")
#print(chm.to.analyze)
chm.to.analyze=chm.to.analyze[order(chm.to.analyze)]
numCHR= length(chm.to.analyze)
#GI.MP[,5]=1:(nrow(GI.MP))
bin.mp=GI.MP[,1:3]
bin.mp[,3]=0 # for r2
bin.mp[,1]=as.numeric(as.vector(GI.MP[,2]))+as.numeric(as.vector(GI.MP[,1]))*(10^(max(GI.MP[,1])+1))
#as.numeric(as.vector(GP[,3]))+as.numeric(as.vector(GP[,2]))*MaxBP
#print(head(bin.mp))
bin.mp[,2]=floor(bin.mp[,1]/plot.bin)
if(!is.null(GD)) X=GD
#print(head(bin.mp))
#Chromosomewise plot
if(plot.type == "Chromosomewise"&!is.null(GD))
{
#print("Manhattan ploting Chromosomewise")
GI.MP=cbind(GI.MP,bin.mp)
pdf(paste("GAPIT.", name.of.trait,".Manhattan.Plot.Chromosomewise.pdf" ,sep = ""), width = 10)
#par(mar = c(5,5,4,3), lab = c(8,5,7))
layout(matrix(c(1,1,2,1,1,1,1,1,1),3,3,byrow=TRUE), c(2,1), c(1,1), TRUE)
for(i in 1:numCHR)
{
#Extract SBP on this chromosome
subset=GI.MP[GI.MP[,1]==chm.to.analyze[i],,drop=FALSE]
# print(head(subset))
if(nrow(subset)==0)next #thanks to lvclark to fix it
subset[,1]=1:(nrow(subset))
#sub.bin.mp=bin.mp[GI.MP[,1]==chm.to.analyze[i],]
#subset=cbind(subset,sub.bin.mp)
sig.mp=subset[subset[,3]>bonferroniCutOff,,drop=FALSE]
sig.index=subset[,3]>bonferroniCutOff ### index of significont SNP
num.row=nrow(sig.mp)
if(!is.null(dim(sig.mp)))sig.mp=sig.mp[!duplicated(sig.mp[,7]),]
num.row=nrow(sig.mp)
if(is.null(dim(sig.mp))) num.row=1
bin.set=NULL
r2_color=matrix(0,nrow(subset),2)
#r2_color
print(paste("select ",num.row," candidate significont markers in ",i," chromosome ",sep="") )
#print(sig.mp)
if(length(unique(sig.index))==2)
{
for(j in 1:num.row)
{ sig.mp=matrix(sig.mp,num.row,8)
#print(sig.mp[j,7])
#print(unique(subset[,7]))
bin.store=subset[which(subset[,7]==sig.mp[j,7]),]
if(is.null(dim(bin.store)))
{subset[which(subset[,7]==sig.mp[j,7]),8]=1
next
}
bin.index=unique(bin.store[,5])
subGD=X[,bin.store[,5]]
#print(dim(bin.store))
if(is.null(CG))candidata=bin.store[bin.store[,3]==max(bin.store[,3]),5]
if(length(candidata)!=1)candidata=candidata[1]
for (k in 1:ncol(subGD))
{
r2=cor(X[,candidata],subGD[,k])^2
#print(r2)
bin.store[k,8]=r2
}
#print(bin.store)
#r2_storage[is.na(r2_storage)]=0
#print(bin.store)
subset[bin.store[,1],8]=bin.store[,8]
#print()
}###end for each sig.mp
#sub.bin.mp=bin.mp[subset[,3]>bonferroniCutOff,]
#print(head(bin.set))
}###end if empty of sig.mp
#print("@@@@@@@@@@@@@@@@")
rm(sig.mp,num.row)
#print(head(subset))
#print(head(subset))
#print(dim(X))
y.lim <- ceiling(max(subset[,3]))+1 #set upper for each chr
if(length(subset)>3){
x <- as.numeric(subset[,2])/10^(6)
y <- as.numeric(subset[,3])
}else{
x <- as.numeric(subset[2])/10^(6)
y <- as.numeric(subset[3])
}
##print(paste("befor prune: chr: ",i, "length: ",length(x),"max p",max(y), "min p",min(y), "max x",max(x), "Min x",min(x)))
n_col=10
r2_color[,2]=subset[,8]
do_color=colorRampPalette(c("orangeRed", "blue"))(n_col)
#Prune most non important SNPs off the plots
order=order(y,decreasing = TRUE)
y=y[order]
x=x[order]
r2_color=r2_color[order,,drop=FALSE]
index=GAPIT.Pruning(y,DPP=round(DPP/numCHR))
x=x[index]
y=y[index]
r2_color=r2_color[index,,drop=FALSE]
r2_color[which(r2_color[,2]<=0.2),2]=do_color[n_col]
r2_color[which(r2_color[,2]<=0.4&r2_color[,2]>0.2),2]=do_color[n_col*0.8]
r2_color[which(r2_color[,2]<=0.6&r2_color[,2]>0.4),2]=do_color[n_col*0.6]
r2_color[which(r2_color[,2]<=0.8&r2_color[,2]>0.6),2]=do_color[n_col*0.4]
r2_color[which(r2_color[,2]<=1&r2_color[,2]>0.8),2]=do_color[n_col/n_col]
#print(unique(r2_color[,2]))
##print(paste("after prune: chr: ",i, "length: ",length(x),"max p",max(y), "min p",min(y), "max x",max(x), "Min x",min(x)))
par(mar=c(0,0,0,0))
par(mar=c(5,5,2,1),cex=0.8)
plot(y~x,type="p", ylim=c(0,y.lim), xlim = c(min(x), max(x)),
col = r2_color[,2], xlab = expression(Base~Pairs~(x10^-6)),
ylab = "-Log Base 10 p-value", main = paste("Chromosome",chm.to.analyze[i],sep=" "),
cex.lab=1.6,pch=21,bg=r2_color[,2])
abline(h=bonferroniCutOff,col="forestgreen")
##print("manhattan plot (chr) finished")
#layout.show(nf)
#provcol <-c("darkblue","cyan","green3","brown1","brown1")
#provcol <-heat.colors(50)
#par(mar=c(0,0,0,0))
par(mar=c(15,5,6,5),cex=0.5)
barplot(matrix(rep(1,times=n_col),n_col,1),beside=T,col=do_color,border=do_color,axes=FALSE,)
#legend(x=10,y=2,legend=expression(R^"2"),,lty=0,cex=1.3,bty="n",bg=par("bg"))
axis(3,seq(11,1,by=-2),seq(0,1,by=0.2))
}# end plot.type == "Chromosomewise"&!is.null(GD)
dev.off()
print("manhattan plot on chromosome finished")
} #Chromosomewise plot
#Genomewise plot
if(plot.type == "Genomewise")
{
#print("Manhattan ploting Genomewise")
#Set corlos for chromosomes
#nchr=max(chm.to.analyze)
nchr=length(chm.to.analyze)
#Set color schem
ncycle=ceiling(nchr/band)
ncolor=band*ncycle
#palette(rainbow(ncolor+1))
cycle1=seq(1,nchr,by= ncycle)
thecolor=cycle1
for(i in 2:ncycle){thecolor=c(thecolor,cycle1+(i-1))}
col.Rainbow=rainbow(ncolor+1)[thecolor]
col.FarmCPU=rep(c("#CC6600","deepskyblue","orange","forestgreen","indianred3"),ceiling(numCHR/5))
col.Rushville=rep(c("orangered","navyblue"),ceiling(numCHR/2))
col.Congress=rep(c("deepskyblue3","firebrick"),ceiling(numCHR/2))
col.Ocean=rep(c("steelblue4","cyan3"),ceiling(numCHR/2))
col.PLINK=rep(c("gray10","gray70"),ceiling(numCHR/2))
col.Beach=rep(c("turquoise4","indianred3","darkolivegreen3","red","aquamarine3","darkgoldenrod"),ceiling(numCHR/5))
#col.Oceanic=rep(c( '#EC5f67', '#F99157', '#FAC863', '#99C794', '#5FB3B3', '#6699CC', '#C594C5', '#AB7967'),ceiling(numCHR/8))
#col.Oceanic=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5', '#AB7967'),ceiling(numCHR/6))
col.Oceanic=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(numCHR/5))
col.cougars=rep(c( '#990000', 'dimgray'),ceiling(numCHR/2))
if(plot.style=="Rainbow")plot.color= col.Rainbow
if(plot.style =="FarmCPU")plot.color= col.Rainbow
if(plot.style =="Rushville")plot.color= col.Rushville
if(plot.style =="Congress")plot.color= col.Congress
if(plot.style =="Ocean")plot.color= col.Ocean
if(plot.style =="PLINK")plot.color= col.PLINK
if(plot.style =="Beach")plot.color= col.Beach
if(plot.style =="Oceanic")plot.color= col.Oceanic
if(plot.style =="cougars")plot.color= col.cougars
#FarmCPU uses filled dots
mypch=1
if(plot.style =="FarmCPU")mypch=20
GI.MP <- GI.MP[order(GI.MP[,2]),]
GI.MP <- GI.MP[order(GI.MP[,1]),]
ticks=NULL
lastbase=0
#print("Manhattan data sorted")
#print(chm.to.analyze)
#change base position to accumulatives (ticks)
for (i in chm.to.analyze)
{
index=(GI.MP[,1]==i)
ticks <- c(ticks, lastbase+mean(GI.MP[index,2]))
GI.MP[index,2]=GI.MP[index,2]+lastbase
lastbase=max(GI.MP[index,2])
}
#print("Manhattan chr processed")
#print(length(index))
#print(length(ticks))
#print((ticks))
#print((lastbase))
x0 <- as.numeric(GI.MP[,2])
y0 <- as.numeric(GI.MP[,3])
z0 <- as.numeric(GI.MP[,1])
position=order(y0,decreasing = TRUE)
index0=GAPIT.Pruning(y0[position],DPP=DPP)
index=position[index0]
x=x0[index]
y=y0[index]
z=z0[index]
#Extract QTN
QTN=GI.MP[which(GI.MP[,borrowSlot]==1),]
#print(QTN)
#Draw circles with same size and different thikness
size=1 #1
ratio=10 #5
base=1 #1
themax=ceiling(max(y))
themin=floor(min(y))
wd=((y-themin+base)/(themax-themin+base))*size*ratio
s=size-wd/ratio/2
#print("Manhattan XY created")
####xiaolei update on 2016/01/09
if(plot.style =="FarmCPU"){
pdf(paste("FarmCPU.", name.of.trait,".Manhattan.Plot.Genomewise.pdf" ,sep = ""), width = 13,height=5.75)
}else{
pdf(paste("GAPIT.", name.of.trait,".Manhattan.Plot.Genomewise.pdf" ,sep = ""), width = 13,height=5.75)
}
par(mar = c(3,6,5,1))
plot(y~x,xlab="",ylab=expression(-log[10](italic(p))) ,
cex.axis=1.5, cex.lab=2, ,col=plot.color[z],axes=FALSE,type = "p",pch=mypch,lwd=wd,cex=s+.3,main = paste(name.of.trait,sep=" "),cex.main=2.5)
#Label QTN positions
if(is.vector(QTN)){
if(position.only){abline(v=QTN[2], lty = 2, lwd=1.5, col = "grey")}else{
points(QTN[2], QTN[3], type="p",pch=21, cex=2,lwd=1.5,col="dimgrey")
points(QTN[2], QTN[3], type="p",pch=20, cex=1,lwd=1.5,col="dimgrey")
}
}else{
if(position.only){abline(v=QTN[,2], lty = 2, lwd=1.5, col = "grey")}else{
points(QTN[,2], QTN[,3], type="p",pch=21, cex=2,lwd=1.5,col="dimgrey")
points(QTN[,2], QTN[,3], type="p",pch=20, cex=1,lwd=1.5,col="dimgrey")
}
}
#Add a horizontal line for bonferroniCutOff
abline(h=bonferroniCutOff,col="forestgreen")
#print(bonferroniCutOff)
#Set axises
# jiabo creat chor_taxa
#print(chor_taxa)
if(length(chor_taxa)!=length(ticks))chor_taxa=NULL
#print(unique(GI.MP[,1]))
if(!is.null(chor_taxa))
{axis(1, at=ticks,cex.axis=1.5,labels=chor_taxa,tick=F)
}else{axis(1, at=ticks,cex.axis=1.5,labels=chm.to.analyze,tick=F)}
axis(2, at=1:themax,cex.axis=1.5,labels=1:themax,tick=F)
box()
palette("default")
dev.off()
#print("Manhattan done Genomewise")
} #Genomewise plot
print("GAPIT.Manhattan accomplished successfully!zw")
} #end of GAPIT.Manhattan
#=============================================================================================
`GAPIT.Memory.Object` <-
function(name.of.trait="Trait"){
# Object: To report memoery usage
# Authors: Heuristic Andrew
# http://heuristically.wordpress.com/2010/01/04/r-memory-usage-statistics-variable/
# Modified by Zhiwu Zhang
# Last update: may 29, 2011
##############################################################################################
# print aggregate memory usage statistics
print(paste('R is using', memory.size(), 'MB out of limit', memory.limit(), 'MB'))
# create function to return matrix of memory consumption
object.sizes <- function()
{
return(rev(sort(sapply(ls(envir=.GlobalEnv), function (object.name)
object.size(get(object.name))))))
}
# export file in table format
memory=object.sizes()
file=paste("GAPIT.", name.of.trait,".Memory.Object.csv" ,sep = "")
write.table(memory, file, quote = FALSE, sep = ",", row.names = TRUE,col.names = TRUE)
# export file in PDF format
pdf(paste("GAPIT.", name.of.trait,".Memory.Object.pdf" ,sep = ""))
# draw bar plot
barplot(object.sizes(),
main="Memory usage by object", ylab="Bytes", xlab="Variable name",
col=heat.colors(length(object.sizes())))
# draw dot chart
dotchart(object.sizes(), main="Memory usage by object", xlab="Bytes")
# draw pie chart
pie(object.sizes(), main="Memory usage by object")
dev.off()
}
#=============================================================================================
`GAPIT.Memory` <-
function(Memory =NULL,Infor){
#Object: To report memory usage
#Output: Memory
#Authors: Zhiwu Zhang
# Last update: June 6, 2011
##############################################################################################
gc()
size <- memory.size()
#print(paste("Memory usage: ",size," for", Infor))
if(is.null(Memory)) {
Increased=0
Memory =cbind(Infor,size ,Increased)
}else{
Increased=0
Memory.current=cbind(Infor,size ,Increased)
Memory=rbind(Memory,Memory.current)
Memory[nrow(Memory),3]=as.numeric(as.matrix(Memory[nrow(Memory),2]))-as.numeric(as.matrix(Memory[nrow(Memory)-1,2]))
}
return (Memory)
}#end of GAPIT.Memory function
#=============================================================================================
`GAPIT.Multiple.Manhattan` <-
function(model_store,DPP=50000,cutOff=0.01,band=5,seqQTN=NULL,Y=NULL,GM=NULL,interQTN=NULL,plot.style="Oceanic",plot.line=FALSE){
#Object: Make a Manhattan Plot
#Options for plot.type = "Separate_Graph_for_Each_Chromosome" and "Same_Graph_for_Each_Chromosome"
#Output: A pdf of the Manhattan Plot
#Authors: Alex Lipka, Zhiwu Zhang, Meng Li and Jiabo Wang
# Last update: Oct 10, 2016
#Add r2 between candidata SNP and other markers in on choromosome
##############################################################################################
Nenviron=length(model_store)*(ncol(Y)-1)
environ_name=NULL
new_xz=NULL
for(i in 1:length(model_store))
{
for(j in 1:(ncol(Y)-1))
{
environ_name=c(environ_name,paste(model_store[i],".",colnames(Y)[-1][j],sep=""))
}
}
sig_pos=NULL
simulation=FALSE
if(!is.null(seqQTN)){
#seqQTN=-seqQTN
simulation=TRUE
}
for(i in 1:length(environ_name))
{
environ_result=read.csv(paste("GAPIT.",environ_name[i],".GWAS.Results.csv",sep=""),head=T)
environ_filter=environ_result[!is.na(environ_result[,4]),]
y_filter=environ_filter[environ_filter[,4]<(cutOff/(nrow(environ_filter))),]
write.table(y_filter,paste("Filter_",environ_name[i],"_GWAS_result.txt",sep=""))
result=environ_result[,1:4]
result=result[match(as.character(GM[,1]),as.character(result[,1])),]
# result=result[order(result[,2]),]
# result=result[order(result[,1]),]
#print(head(result))
rownames(result)=1:nrow(result)
#print(i)
if(i==1){
result0=result
colnames(result0)[4]=environ_name[i]
}
if(i!=1){
result0=merge(result0,result[,c(1,4)],by.x=colnames(result0)[1],by.y=colnames(result)[1])
colnames(result0)[i+3]=environ_name[i]
}
rownames(result)=1:nrow(result)
result[is.na(result[,4]),4]=1
sig_pos=append(sig_pos,as.numeric(rownames(result[result[!is.na(result[,4]),4]<(cutOff/nrow(result)),])))
}
#if(length(sig_pos)!=0)sig_pos=sig_pos[!duplicated(sig_pos)]
if(length(sig_pos[!is.na(sig_pos)])!=0)
{ x_matrix=as.matrix(table(sig_pos))
x_matrix=cbind(as.data.frame(rownames(x_matrix)),x_matrix)
#print(x_matrix)
lastbase=0
map_store=as.matrix(cbind(as.numeric(GM[,2]),as.numeric(as.vector(GM[,3]))))
#print(head(map_store))
#print(as.numeric(map_store[,3]))
for (j in unique(map_store[,1]))
{
index=map_store[,1]==j
#print(table(index))
map_store[index,2]=as.numeric(map_store[index,2])+lastbase
lastbase=max(as.numeric(map_store[index,2]))
#print(lastbase)
}
colnames(x_matrix)=c("pos","times")
#colnames(xz)=c("pos","col")
new_xz=cbind(x_matrix,map_store[as.numeric(as.character(x_matrix[,1])),])
#new_xz[,4]=0
colnames(new_xz)=c("pos","times","chro","xlab")
new_xz=new_xz[!duplicated(new_xz),]
new_xz[new_xz[,2]>=3,2]=3
new_xz[,2]=4-new_xz[,2]
new_xz[new_xz[,2]==3,2]=0
new_xz=as.matrix(new_xz)
new_xz=new_xz[new_xz[,2]!="0",]
new_xz=matrix(new_xz,length(as.vector(new_xz))/4,4)
#print(new_xz)
plot.line=TRUE
#print(new_xz)
}
#print(as.numeric(new_xz[,4]))
#print(head(result0))
# print(as.numeric(new_xz[,1]))
pdf(paste("GAPIT.Manhattan.Mutiple.Plot",colnames(result0)[-c(1:3)],".pdf" ,sep = ""), width = 20,height=6*Nenviron)
par(mfrow=c(Nenviron,1))
for(k in 1:Nenviron)
{ if(k==Nenviron){#par(mfrow=c(Nenviron,1))
par(mar = c(3,8,1,8))
}else{
#par(mfrow=c(Nenviron,1))
par(mar = c(0,8,1,8))
}
environ_result=read.csv(paste("GAPIT.",environ_name[k],".GWAS.Results.csv",sep=""),head=T)
#print(environ_result[as.numeric(new_xz[,1]),])
result=environ_result[,1:4]
result=result[match(as.character(GM[,1]),as.character(result[,1])),]
rownames(result)=1:nrow(result)
GI.MP=result[,c(2:4)]
borrowSlot=4
GI.MP[,borrowSlot]=0 #Inicial as 0
GI.MP[,5]=1:(nrow(GI.MP))
GI.MP[,6]=1:(nrow(GI.MP))
GI.MP <- GI.MP[!is.na(GI.MP[,1]),]
GI.MP <- GI.MP[!is.na(GI.MP[,2]),]
GI.MP[is.na(GI.MP[,3]),3]=1
#Retain SNPs that have P values between 0 and 1 (not na etc)
GI.MP <- GI.MP[GI.MP[,3]>0,]
GI.MP <- GI.MP[GI.MP[,3]<=1,]
#Remove chr 0 and 99
GI.MP <- GI.MP[GI.MP[,1]!=0,]
total_chromo=max(GI.MP[,1])
# print(dim(GI.MP))
if(!is.null(seqQTN))GI.MP[seqQTN,borrowSlot]=1
numMarker=nrow(GI.MP)
bonferroniCutOff=-log10(cutOff/numMarker)
GI.MP[,3] <- -log10(GI.MP[,3])
GI.MP[,5]=1:numMarker
y.lim <- ceiling(max(GI.MP[,3]))
chm.to.analyze <- unique(GI.MP[,1])
chm.to.analyze=chm.to.analyze[order(chm.to.analyze)]
nchr=length(chm.to.analyze)
GI.MP[,6]=1:(nrow(GI.MP))
MP_store=GI.MP
index_GI=MP_store[,3]>=0
MP_store <- MP_store[index_GI,]
ticks=NULL
lastbase=0
for (i in chm.to.analyze)
{
index=(MP_store[,1]==i)
ticks <- c(ticks, lastbase+mean(MP_store[index,2]))
MP_store[index,2]=MP_store[index,2]+lastbase
lastbase=max(MP_store[index,2])
}
x0 <- as.numeric(MP_store[,2])
y0 <- as.numeric(MP_store[,3])
z0 <- as.numeric(MP_store[,1])
x1=sort(x0)
position=order(y0,decreasing = TRUE)
values=y0[position]
if(length(values)<=DPP)
{
index=position[c(1:length(values))]
}else{
values=sqrt(values) #This shift the weight a little bit to the low building.
#Handler of bias plot
rv=runif(length(values))
values=values+rv
values=values[order(values,decreasing = T)]
theMin=min(values)
theMax=max(values)
range=theMax-theMin
interval=range/DPP
ladder=round(values/interval)
ladder2=c(ladder[-1],0)
keep=ladder-ladder2
index=position[which(keep>=0)]
}
x=x0[index]
y=y0[index]
z=z0[index]
# print(length(x))
#Extract QTN
#if(!is.null(seqQTN))MP_store[seqQTN,borrowSlot]=1
#if(!is.null(interQTN))MP_store[interQTN,borrowSlot]=2
QTN=MP_store[which(MP_store[,borrowSlot]==1),]
#Draw circles with same size and different thikness
size=1 #1
ratio=10 #5
base=1 #1
numCHR=nchr
themax=ceiling(max(y))
themin=floor(min(y))
wd=((y-themin+base)/(themax-themin+base))*size*ratio
s=size-wd/ratio/2
ncycle=ceiling(nchr/5)
ncolor=5*ncycle
ncolor=band*ncycle
thecolor=seq(1,nchr,by= ncycle)
mypch=1
#plot.color= rainbow(ncolor+1)
col.Rainbow=rainbow(ncolor+1)
col.FarmCPU=rep(c("#CC6600","deepskyblue","orange","forestgreen","indianred3"),ceiling(numCHR/5))
col.Rushville=rep(c("orangered","navyblue"),ceiling(numCHR/2))
col.Congress=rep(c("deepskyblue3","firebrick"),ceiling(numCHR/2))
col.Ocean=rep(c("steelblue4","cyan3"),ceiling(numCHR/2))
col.PLINK=rep(c("gray10","gray70"),ceiling(numCHR/2))
col.Beach=rep(c("turquoise4","indianred3","darkolivegreen3","red","aquamarine3","darkgoldenrod"),ceiling(numCHR/5))
#col.Oceanic=rep(c( '#EC5f67', '#F99157', '#FAC863', '#99C794', '#5FB3B3', '#6699CC', '#C594C5', '#AB7967'),ceiling(numCHR/8))
#col.Oceanic=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5', '#AB7967'),ceiling(numCHR/6))
col.Oceanic=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(numCHR/5))
col.cougars=rep(c( '#990000', 'dimgray'),ceiling(numCHR/2))
if(plot.style=="Rainbow")plot.color= col.Rainbow
if(plot.style =="FarmCPU")plot.color= col.Rainbow
if(plot.style =="Rushville")plot.color= col.Rushville
if(plot.style =="Congress")plot.color= col.Congress
if(plot.style =="Ocean")plot.color= col.Ocean
if(plot.style =="PLINK")plot.color= col.PLINK
if(plot.style =="Beach")plot.color= col.Beach
if(plot.style =="Oceanic")plot.color= col.Oceanic
if(plot.style =="cougars")plot.color= col.cougars
#plot.color=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(ncolor/5))
plot(y~x,xlab="",ylab="" ,ylim=c(0,themax),
cex.axis=4, cex.lab=4, ,col=plot.color[z],axes=FALSE,type = "p",pch=mypch,lwd=wd,cex=s+2.5,cex.main=4)
mtext(side=2,expression(-log[10](italic(p))),line=3, cex=2.5)
#Label QTN positions
#print(head(QTN))
#print(head(interQTN))
if(!simulation){abline(v=QTN[2], lty = 2, lwd=1.5, col = "grey")}else{
#print("$$$$$$")
points(QTN[,2], QTN[,3], pch=20, cex=2.5,lwd=2.5,col="black")
#points(interQTN[,2], interQTN[,3], type="p",pch=8, cex=1,lwd=1.5,col="dimgrey")
}
#}
if(plot.line){
#print(x)
#print(as.numeric(new_xz[,2]))
# if(!is.null(nrow(new_xz))) {abline(v=as.numeric(new_xz[,4]),col=plot.color[as.numeric(new_xz[,3])],lty=as.numeric(new_xz[,2]),untf=T,lwd=3)
if(!is.null(nrow(new_xz))) {abline(v=as.numeric(new_xz[,4]),col="grey",lty=as.numeric(new_xz[,2]),untf=T,lwd=3)
}else{abline(v=as.numeric(new_xz[1]),col=plot.color[as.numeric(new_xz[3])],lty=as.numeric(new_xz[2]),untf=T,lwd=3)
}
}
#Add a horizontal line for bonferroniCutOff
abline(h=bonferroniCutOff,lty=2,untf=T,lwd=3,col="red")
axis(2, xaxp=c(1,themax,5),cex.axis=2.5,tick=F)
if(k==Nenviron)axis(1, at=ticks,cex.axis=2.7,labels=chm.to.analyze,tick=F)
mtext(side=4,paste(environ_name[k],sep=""),line=3,cex=2.5)
box()
}#end of environ_name
dev.off()
print("GAPIT.Manhattan.Mutiple.Plot has done !!!")
return(list(multip_mapP=result0,xz=new_xz))
} #end of GAPIT.Manhattan
#=============================================================================================
`GAPIT.Numericalization` <-
function(x,bit=2,effect="Add",impute="None", Create.indicator = FALSE, Major.allele.zero = FALSE, byRow=TRUE){
#Object: To convert character SNP genotpe to numerical
#Output: Coresponding numerical value
#Authors: Feng Tian and Zhiwu Zhang
# Last update: May 30, 2011
##############################################################################################
if(bit==1) {
x[x=="X"]="N"
x[x=="-"]="N"
x[x=="+"]="N"
x[x=="/"]="N"
x[x=="K"]="Z" #K (for GT genotype)is replaced by Z to ensure heterozygose has the largest value
}
if(bit==2) {
x[x=="XX"]="N"
x[x=="--"]="N"
x[x=="++"]="N"
x[x=="//"]="N"
x[x=="NN"]="N"
x[x=="00"]="N"
}
n=length(x)
lev=levels(as.factor(x))
lev=setdiff(lev,"N")
#print(lev)
len=length(lev)
#print(len)
#Jiabo creat this code to convert AT TT to 1 and 2. 2018.5.29
if(bit==2)
{
inter_store=c("AT","AG","AC","TA","GA","CA","GT","TG","GC","CG","CT","TC")
inter=intersect(lev,inter_store)
if(length(inter)>1)
{
x[x==inter[2]]=inter[1]
n=length(x)
lev=levels(as.factor(x))
lev=setdiff(lev,"N")
#print(lev)
len=length(lev)
}
if(len==2&bit==2)
{ #inter=intersect(lev,inter_store)
if(!is.na(inter[1]))
{
lev=union(lev,"UU")
len=len+1
}
}
if(len==3&bit==2)
{
inter=intersect(lev,inter_store)
}
}
#print(lev)
#print(len)
#Jiabo code is end here
#Genotype counts
count=1:len
for(i in 1:len){
count[i]=length(x[(x==lev[i])])
}
#print(count)
if(Major.allele.zero){
if(len>1 & len<=3){
#One bit: Make sure that the SNP with the major allele is on the top, and the SNP with the minor allele is on the second position
if(bit==1){
count.temp = cbind(count, seq(1:len))
if(len==3) count.temp = count.temp[-3,]
count.temp <- count.temp[order(count.temp[,1], decreasing = TRUE),]
if(len==3)order = c(count.temp[,2],3)else order = count.temp[,2]
}
#Two bit: Make sure that the SNP with the major allele is on the top, and the SNP with the minor allele is on the third position
if(bit==2){
count.temp = cbind(count, seq(1:len))
if(len==3) count.temp = count.temp[-2,]
count.temp <- count.temp[order(count.temp[,1], decreasing = TRUE),]
if(len==3) order = c(count.temp[1,2],2,count.temp[2,2])else order = count.temp[,2]
}
count = count[order]
lev = lev[order]
} #End if(len<=1 | len> 3)
} #End if(Major.allele.zero)
#print(x)
#make two bit order genotype as AA,AT and TT, one bit as A(AA),T(TT) and X(AT)
if(bit==1 & len==3){
temp=count[2]
count[2]=count[3]
count[3]=temp
}
#print(lev)
#print(count)
position=order(count)
#Jiabo creat this code to convert AT TT to 1 and 2.2018.5.29
lev1=lev
if(bit==2&len==3)
{
lev1[1]=lev[count==sort(count)[1]]
lev1[2]=lev[count==sort(count)[2]]
lev1[3]=lev[count==sort(count)[3]]
position=c(1:3)
lev=lev1
}
#print(lev)
#print(position)
#print(inter)
#Jiabo code is end here
#1status other than 2 or 3
if(len<=1 | len> 3)x=0
#2 status
if(len==2)x=ifelse(x=="N",NA,ifelse(x==lev[1],0,2))
#3 status
if(bit==1){
if(len==3)x=ifelse(x=="N",NA,ifelse(x==lev[1],0,ifelse(x==lev[3],1,2)))
}else{
if(len==3)x=ifelse(x=="N",NA,ifelse(x==lev[lev!=inter][1],0,ifelse(x==inter,1,2)))
}
#print(paste(lev,len,sep=" "))
#print(position)
#missing data imputation
if(impute=="Middle") {x[is.na(x)]=1 }
if(len==3){
if(impute=="Minor") {x[is.na(x)]=position[1] -1}
if(impute=="Major") {x[is.na(x)]=position[len]-1}
}else{
if(impute=="Minor") {x[is.na(x)]=2*(position[1] -1)}
if(impute=="Major") {x[is.na(x)]=2*(position[len]-1)}
}
#alternative genetic models
if(effect=="Dom") x=ifelse(x==1,1,0)
if(effect=="Left") x[x==1]=0
if(effect=="Right") x[x==1]=2
if(byRow) {
result=matrix(x,n,1)
}else{
result=matrix(x,1,n)
}
return(result)
}#end of GAPIT.Numericalization function
#=============================================================================================
`GAPIT.PCA` <-
function(X,taxa, PC.number = min(ncol(X),nrow(X)),file.output=TRUE,PCA.total=0,PCA.col=NULL,PCA.3d=FALSE){
# Object: Conduct a principal component analysis, and output the prinicpal components into the workspace,
# a text file of the principal components, and a pdf of the scree plot
# Authors: Alex Lipka and Hyun Min Kang
# Last update: May 31, 2011
##############################################################################################
#Conduct the PCA
print("Calling prcomp...")
PCA.X <- prcomp(X)
eigenvalues <- PCA.X$sdev^2
evp=eigenvalues/sum(eigenvalues)
nout=min(10,length(evp))
xout=1:nout
if(is.null(PCA.col)) PCA.col="red"
print("Creating PCA graphs...")
#Create a Scree plot
if(file.output & PC.number>1) {
pdf("GAPIT.PCA.eigenValue.pdf", width = 12, height = 12)
par(mar=c(5,5,4,5)+.1,cex=2)
#par(mar=c(10,9,9,10)+.1)
plot(xout,eigenvalues[xout],type="b",col="blue",xlab="Principal components",ylab="Variance")
par(new=TRUE)
plot(xout,evp[xout]*100,type="n",col="red",xaxt="n",yaxt="n",xlab="",ylab="")
axis(4)
mtext("Percentage (%)",side=4,line=3,cex=2)
dev.off()
pdf("GAPIT.PCA.2D.pdf", width = 8, height = 8)
par(mar = c(5,5,5,5))
maxPlot=min(as.numeric(PC.number[1]),3)
for(i in 1:(maxPlot-1)){
for(j in (i+1):(maxPlot)){
plot(PCA.X$x[,i],PCA.X$x[,j],xlab=paste("PC",i,sep=""),ylab=paste("PC",j,sep=""),pch=19,col=PCA.col,cex.axis=1.3,cex.lab=1.4, cex.axis=1.2, lwd=2,las=1)
}
}
dev.off()
#output 3D plot
if(PCA.3d==TRUE)
{
if(1>2)
{if(!require(lattice)) install.packages("lattice")
library(lattice)
pca=as.data.frame(PCA.X$x)
png(file="example%03d.png", width=500, heigh=500)
for (i in seq(10, 80 , 1)){
print(cloud(PC1~PC2*PC3,data=pca,screen=list(x=i,y=i-40),pch=20,color="red",
col.axis="blue",cex=1,cex.lab=1.4, cex.axis=1.2,lwd=3))
}
dev.off()
system("convert -delay 40 *.png GAPIT.PCA.3D.gif")
# cleaning up
file.remove(list.files(pattern=".png"))
}
if(!require(rgl)) install.packages("rgl")
if(!require(rglwidget)) install.packages("rglwidget")
library(rgl)
PCA1 <- PCA.X$x[,1]
PCA2 <- PCA.X$x[,2]
PCA3 <- PCA.X$x[,3]
plot3d(PCA1, PCA2, PCA3, col = "white",radius=0.01)
num_col=length(unique(PCA.col))
if(num_col==1)
{
sids1 <- spheres3d(PCA1, PCA2, PCA3, col = PCA.col,radius=1)
widgets<-rglwidget(width = 900, height = 900) %>%toggleWidget(ids = sids1, label = "PCA")
}else if(num_col==2)
{
index1=PCA.col==unique(PCA.col)[1]
index2=PCA.col==unique(PCA.col)[2]
sids1 <- spheres3d(PCA1[index1], PCA2[index1], PCA3[index1], col = PCA.col[index1],radius=1)
sids2 <- spheres3d(PCA1[index2], PCA2[index2], PCA3[index2], col = PCA.col[index2],radius=1)
widgets<-rglwidget(width = 900, height = 900) %>%toggleWidget(ids = sids1, label = "Population 1")%>%toggleWidget(ids = sids2, label = "Population 2")
}else if(num_col==3)
{
index1=PCA.col==unique(PCA.col)[1]
index2=PCA.col==unique(PCA.col)[2]
index3=PCA.col==unique(PCA.col)[3]
sids1 <- spheres3d(PCA1[index1], PCA2[index1], PCA3[index1], col = PCA.col[index1],radius=1)
sids2 <- spheres3d(PCA1[index2], PCA2[index2], PCA3[index2], col = PCA.col[index2],radius=1)
sids3 <- spheres3d(PCA1[index3], PCA2[index3], PCA3[index3], col = PCA.col[index3],radius=1)
widgets<-rglwidget(width = 900, height = 900) %>%toggleWidget(ids = sids1, label = "Population 1")%>%toggleWidget(ids = sids2, label = "Population 2")%>%toggleWidget(ids = sids3, label = "Population 3")
}else if(num_col==4)
{
index1=PCA.col==unique(PCA.col)[1]
index2=PCA.col==unique(PCA.col)[2]
index3=PCA.col==unique(PCA.col)[3]
index4=PCA.col==unique(PCA.col)[4]
sids1 <- spheres3d(PCA1[index1], PCA2[index1], PCA3[index1], col = PCA.col[index1],radius=1)
sids2 <- spheres3d(PCA1[index2], PCA2[index2], PCA3[index2], col = PCA.col[index2],radius=1)
sids3 <- spheres3d(PCA1[index3], PCA2[index3], PCA3[index3], col = PCA.col[index3],radius=1)
sids4 <- spheres3d(PCA1[index4], PCA2[index4], PCA3[index4], col = PCA.col[index4],radius=1)
widgets<-rglwidget(width = 900, height = 900) %>%toggleWidget(ids = sids1, label = "Population 1")%>%toggleWidget(ids = sids2, label = "Population 2")%>%toggleWidget(ids = sids3, label = "Population 3")%>%toggleWidget(ids = sids4, label = "Population 4")
}
if (interactive()) widgets
htmltools::save_html(widgets, "Interactive.PCA.html")
}
if(!require(scatterplot3d)) install.packages("scatterplot3d")
library(scatterplot3d)
pdf("GAPIT.PCA.3D.pdf", width = 7, height = 7)
par(mar = c(5,5,5,5))
scatterplot3d(PCA.X$x[,1],PCA.X$x[,2],PCA.X$x[,3],xlab=paste("PC",1,sep=""),ylab=paste("PC",2,sep=""),zlab=paste("PC",3,sep="") ,pch=20,color=PCA.col,col.axis="blue",cex=1,cex.lab=1.4, cex.axis=1.2,lwd=3,angle=55,scale.y=0.7)
dev.off()
}
print("Joining taxa...")
#Extract number of PCs needed
PCs <- cbind(taxa,as.data.frame(PCA.X$x))
#Remove duplicate (This is taken care by QC)
#PCs.unique <- unique(PCs[,1])
#PCs <-PCs[match(PCs.unique, PCs[,1], nomatch = 0), ]
print("Exporting PCs...")
#Write the PCs into a text file
if(file.output) write.table(PCs[,1:(PCA.total+1)], "GAPIT.PCA.csv", quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
if(file.output) write.table(PCA.X$rotation[,1:PC.number], "GAPIT.PCA.loadings.csv", quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
if(file.output) write.table(eigenvalues, "GAPIT.PCA.eigenvalues.csv", quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#Return the PCs
return(list(PCs=PCs,EV=PCA.X$sdev^2,nPCs=NULL))
}
#=============================================================================================
`GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure` <-
function(PWI = PWI, FDR.Rate = 0.05, FDR.Procedure = "BH"){
#Object: Conduct the Benjamini-Hochberg FDR-Controlling Procedure
#Output: PWIP, number.of.significant.SNPs
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: May 5, 2011
##############################################################################################
#Make sure that your compouter has the latest version of Bioconductor (the "Biobase" package) and multtest
if(is.null(PWI))
{
PWIP=NULL
number.of.significant.SNPs = 0
}
if(!is.null(PWI))
{
#library(multtest)
if(dim(PWI)[1] == 1){
PWIP <- cbind(PWI, PWI[4])
colnames(PWIP)[9] <- "FDR_Adjusted_P-values"
}
if(dim(PWI)[1] > 1){
#mt.rawp2adjp Performs the Simes procedure. The output should be two columns, Left column: originial p-value
#Right column: Simes corrected p-value
res <- mt.rawp2adjp(PWI[,4], FDR.Procedure)
#This command should order the p-values in the order of the SNPs in the data set
adjp <- res$adjp[order(res$index), ]
#round(adjp[1:7,],4)
#Logical statment: 0, if Ho is not rejected; 1, if Ho is rejected, by the Simes corrected p-value
# temp <- mt.reject(adjp[,2], FDR.Rate)
#Lists all number of SNPs that were rejected by the BY procedure
#temp$r
#Attach the FDR adjusted p-values to AS_Results
PWIP <- cbind(PWI, adjp[,2])
#Sort these data by lowest to highest FDR adjusted p-value
PWIP <- PWIP[order(PWIP[,4]),]
colnames(PWIP)[9] <- "FDR_Adjusted_P-values"
# number.of.significant.SNPs = temp$r
}
#print("GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure accomplished successfully!")
}
#return(list(PWIP=PWIP, number.of.significant.SNPs = number.of.significant.SNPs))
return(list(PWIP=PWIP))
}#GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure ends here
#=============================================================================================
`GAPIT.Phenotype.PCA.View` <-function(PC=NULL,myY=NULL){
# Object: Analysis PCA effection for Phenotype data ,result:a pdf of the scree plot
# myG:Genotype data
# myY:Phenotype data
# Authors: You Tang
# Last update: Sep 7, 2015
##############################################################################################
print("GAPIT.Phenotype.PCA.View")
if(is.null(PC)){stop("Validation Invalid. Please input four PC value !")}
if(is.null(myY)){stop("Validation Invalid. Please select read valid Phenotype flies !")}
y<-myY[!is.na(myY[,2]),c(1:2)]
traitname=colnames(y)[2]
cv1<-PC[!is.na(match(PC[,1],y[,1])),]
y1<-y[!is.na(match(y[,1],cv1[,1])),]
y2<-y1[order(y1[,1]),]
cv2<-cv1[order(cv1[,1]),]
lcor=round(cor(y2[,-1],cv2[,-1])*100)/100
y.range=max(y2[,2])-min(y2[,2])
y.mean=mean(y2[,2])
n.col=54
y.int=round(abs(y2[,2]-y.mean)/y.range*(.5*n.col-1)*2)+1
mycol=rainbow(n.col)
y.col=mycol[y.int]
y.lab=paste("PC",seq(1:4)," (r=",lcor,")",sep="")
pdf(paste("GAPIT.",traitname,"_vs_PC.pdf",sep=""), width =9, height = 6)
#par(mar = c(5,5,5,5))
par(mar = c(5,5,2,2))
par(mfrow=c(2,2))
plot(y2[,2],cv2[,2],bg="lightgray",xlab="Phenotype",ylab=y.lab[1],main="",cex.lab=1.4,col=y.col)
if(ncol(PC)>2) plot(y2[,2],cv2[,3],bg="lightgray",xlab="Phenotype",ylab=y.lab[2],main="",cex.lab=1.4,col=y.col)
if(ncol(PC)>3) plot(y2[,2],cv2[,4],bg="lightgray",xlab="Phenotype",ylab=y.lab[3],main="",cex.lab=1.4,col=y.col)
if(ncol(PC)>4) plot(y2[,2],cv2[,5],bg="lightgray",xlab="Phenotype",ylab=y.lab[4],main="",cex.lab=1.4,col=y.col)
dev.off()
print(paste("GAPIT.Phenotype.PCA.View ", ".output pdf generate.","successfully!" ,sep = ""))
#GAPIT.Phenotype.View
}
#=============================================================================================
`GAPIT.Phenotype.Simulation` <-
function(GD,GM=NULL,h2=.75,NQTN=10,QTNDist="normal",effectunit=1,category=1,r=0.25,CV,cveff=NULL,a2=0,adim=2){
#Object: To simulate phenotype from genotye
#Input: GD - n by m +1 dataframe or n by m big.matrix
#intput: h2 - heritability
#intput: NQTN - number of QTNs
#intput: QTNDist - Distribution of QTN, options are "geometry", "normal"
#intput: effectunit - effect of fitst QTN, the nect effect is its squre
#intput: theSeed - seed for randomization
#Output: Y,U,E,QTN.Position, and effect
#Straitegy: NA
#Authors: Qishan Wang and Zhiwu Zhang
#Start date: April 4, 2013
#Last update: April 4, 2013
#Set orientation
#Strategy: the number of rows in GD and GM are the same if GD has SNP as row
##############################################################################################
#print("GAPIT.Phenotype.Simulation")
nm=ncol(GD)-1 #Initial by assume GD has snp in col
if(!is.null(GM)) nm=nrow(GM)
ngd1=nrow(GD)
ngd2=ncol(GD)
ngd1=abs(ngd1-nm)
ngd2=abs(ngd2-nm)
orientation="row"
ns=ncol(GD)
if(min(ngd1,ngd2)>0){
orientation="col"
ns=nrow(GD)
}
n= ns #number of samples
m=nm #number of markers
#Set QTN effects
if (QTNDist=="normal"){ addeffect<-rnorm(NQTN,0,1)
}else
{addeffect=effectunit^(1:NQTN)}
#Simulating Genetic effect
#r=sample(2:m,NQTN,replace=F)
QTN.position=sample(1:m,NQTN,replace=F)
if(orientation=="col") SNPQ=as.matrix(GD[,(QTN.position+1)])
if(orientation=="row") SNPQ=t(as.matrix(GD[QTN.position,]))
#Replace non-variant QTNs (does not work yet)
#inComplete=TRUE
#while(inComplete){
# inComplete=FALSE
# myVar=apply(SNPQ,2,var)
# index=which(myVar==0)
# nInVar=length(index)
# if(nInVar>0){
# inComplete=TRUE
# New.position=sample(1:m,nInVar,replace=F)
# if(orientation=="col") SNPQ[,index]=as.matrix(GD[,(New.position+1)])
# if(orientation=="row") SNPQ[,index]=t(as.matrix(GD[New.position,]))
# }
#}#end of while
effect=SNPQ%*%addeffect
effectvar=var(effect)
#Interaction
cp=0*effect
nint= adim
if(a2>0&NQTN>=nint){
for(i in nint:nint){
Int.position=sample(NQTN,i,replace=F)
cp=apply(SNPQ[,Int.position],1,prod)
}
cpvar=var(cp)
intvar=(effectvar-a2*effectvar)/a2
if(is.na(cp[1]))stop("something wrong in simulating interaction")
if(cpvar>0){
#print(c(effectvar,intvar,cpvar,var(cp),a2))
#print(dim(cp))
cp=cp/sqrt(cpvar)
cp=cp*sqrt(intvar)
effectvar=effectvar+intvar
}else{cp=0*effect}
}
#Residual variance
if(h2 >0){
residualvar=(effectvar-h2*effectvar)/h2
}else{
residualvar=1
effect= effect*0
}
#Variance explained by each SNP
effectInd=SNPQ%*%diag(addeffect)
varInd=apply(effectInd,2,var)
effectSeq=order(varInd,decreasing = TRUE)
#Simulating Residual and phenotype
residual=rnorm(n,0,sqrt(residualvar))
#environment effect
if(!is.null(cveff)){
#print(cveff)
vy=effectvar+residualvar
#print(vy)
ev=cveff*vy/(1-cveff)
ec=sqrt(ev)/sqrt(diag(var(CV[,-1])))
enveff=as.matrix(myCV[,-1])%*%ec
#print(cbind(effectvar,residualvar,ev,ec))
#print(cbind(effect,enveff,residual))
residual=residual+enveff
}
#Simulating phenotype
y=effect+residual+cp
if(orientation=="col") myY=cbind(as.data.frame(GD[,1]),as.data.frame(y))
if(orientation=="row") myY=cbind(NA,as.data.frame(y))
#Convert to category phenotype
if(category>1){
myQuantile =(0:category)/category
y.num= myY[,2]
cutoff=quantile(y.num, myQuantile)
y.cat= .bincode(y.num,cutoff,include.lowest = T)
myY[,2]=y.cat
}
#Binary phenotype
if(category==0){
#Standardization
#print("Binary phenotype")
#print(mean(effect))
#print(sqrt(effectvar))
#print(dim(effect))
x=(effect-mean(effect))
x=x/as.numeric(sqrt(effectvar))
myF=GAPIT.BIPH(x,h2=h2,r=r)
p=runif(n)
index=p<myF
myY[index,2]=1
myY[!index,2]=0
}
#print("Phenotype simulation accoplished")
return(list(Y=myY,u=effect,i=cp,e=residual,QTN.position=QTN.position,effect=addeffect))
} #enf of phenotype simulation function
#=============================================================================================
`GAPIT.Phenotype.View` <-function(myY=NULL,traitname="_",memo="_"){
# Object: Analysis for Phenotype data:Distribution of density,Accumulation,result:a pdf of the scree plot
# myY:Phenotype data
# Authors: You Tang
# Last update: Sep 7, 2015
##############################################################################################
print("GAPIT.Phenotype.View in press...")
if(is.null(myY)){stop("Validation Invalid. Please select read valid Phenotype flies !")}
y<-myY[!is.na(myY[,2]),2]
obs<-as.matrix(y)
traitname=colnames(myY)[2]
pdf(paste("GAPIT",memo,traitname,"phenotype_view.pdf",sep ="."), width =10, height = 6)
par(mar = c(5,5,5,5))
par(mfrow=c(2,2))
plot(obs,pch=1)
#hist(obs)
hist(obs,xlab="Density",main="",breaks=12, cex.axis=1,col = "gray")
boxplot(obs)
plot(ecdf(obs),col="red",bg="lightgray",xlab="Density",ylab="Accumulation",main="")
dev.off()
print(paste("GAPIT.Phenotype.View ", ".output pdf generate.","successfully!" ,sep = ""))
#GAPIT.Phenotype.View
}
#=============================================================================================
`GAPIT.Power` <-
function(WS=c(1e0,1e3,1e4,1e5,1e6,1e7), GM=NULL,seqQTN=NULL,GWAS=NULL,maxOut=100,
alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),MaxBP=1e10){
#Object: To evaluate power and FDR for the top (maxOut) positive interval defined by WS
#Input: WS- window size
#Input: GM - m by 3 matrix for SNP name, chromosome and BP
#Input: seqQTN - s by 1 vecter for index of QTN on GM (+1 for GDP column wise)
#Input: GWAS- SNP,CHR,BP,P,MAF
#maxOut: maximum number of rows to report
#Requirement: None
#Output: Table and Plots
#Authors: Zhiwu Zhang
# Date start: April 2, 2013
# Last update: April 2, 2013
##############################################################################################
#print("GAPIT.Power Started")
if(is.null(seqQTN) | is.null(GM) | is.null(GWAS)) return(list(FDR=NULL,Power=NULL,Power.Alpha=NULL,alpha=NULL))
#-----------------FDR and Power analysis-------------------------
#Information needed: myGAPIT$GWAS,myGM and QTN(r)
nWin=matrix(NA,length(WS),1)
format_GWAS=cbind(GWAS[,1:4],NA,NA,NA)
names(format_GWAS)<-c("SNP","Chromosome","Position","P.value","maf","nobs","FDR_Adjusted_P-values")
myGM=GM
#loop window size here
theWS=1
for (theWS in 1:length(WS)){
ws=WS[theWS]
#Label QTN intervals
#Restore original order
#QTNList=r-1
QTNList=seqQTN
myGM2=cbind(myGM,rep(0,nrow(myGM)),1:nrow(myGM),NA) #Initial QTN status as 0
#Extract QTN positions
myGM2[,6]=floor((as.numeric(as.character(myGM2[,2]))*MaxBP+as.numeric(as.character(myGM2[,3])))/ws) #Label QTN as 1
QTNInterval=myGM2[QTNList,6]
thePosition=myGM2[,6] %in% QTNInterval
myGM2[thePosition,4]=1 #Label QTN as 1
names(myGM2) <- c("SNP","Chromosome","Position", "QTN","Seq")
#Merge to P vlaues
#GWAS<- merge(myGAPIT$GWAS[,1:7],myGM2[,c(1,4,5)],by="SNP")
GWAS<- merge(format_GWAS[,1:7],myGM2[,c(1,4,5)],by="SNP")#xiaoalei changed
#checking
#zw=GWAS[order(GWAS[,4],decreasing = FALSE),]
#zw=GWAS[order(GWAS[,8],decreasing = TRUE),]
#head(zw)
#Creat windows
myQTN=GAPIT.Specify(GI=GWAS[,1:3],GP=GWAS,bin.size=ws,MaxBP=MaxBP)
QTN=GWAS[myQTN$index,]
#Calculate alpha
qtnLoc=which(QTN[,8]==1) #get the position of QTN
P.QTN=QTN[qtnLoc,4] #p value of QTN
P.marker=QTN[-qtnLoc,4] #p value of non qtn (marker)
cutOff=matrix(quantile(P.marker, alpha,na.rm=TRUE),ncol=1)#xiaoalei changed
myPower.Alpha=apply(cutOff,1,function(x){
Power=length(which(P.QTN<x))/length(P.QTN)
})
#Sort on P
#QTN=QTN[order(as.numeric(as.character(QTN[,3])),decreasing = FALSE),]
#QTN=QTN[order(as.numeric(as.character(QTN[,2])),decreasing = FALSE),]
QTN=QTN[order(as.numeric(as.character(QTN[,4])),decreasing = FALSE),]
names(QTN) <- c("SNP","Chromosome","Position", "P","FDR","Power","Order","QTN","Seq")
#calculate power
QTN[,7]=1:nrow(QTN)
QTN[,5]=cumsum(1-QTN[,8])/QTN[,7] #FDR
QTN[,6]=cumsum(QTN[,8]) /sum(QTN[,8] ) #Power
#Save results
if (theWS==1){
nWin=matrix(NA,length(WS),1)
FDR=array(NA,dim=c(nrow(QTN),length(WS)))
Power=array(NA,dim=c(nrow(QTN),length(WS)))
Power.Alpha=array(NA,dim=c(length(alpha),length(WS)))
}
nWin[theWS]=nrow(QTN)
FDR[1:nWin[theWS],theWS]=QTN[,5]
Power[1:nWin[theWS],theWS]=QTN[,6]
Power.Alpha[,theWS]=myPower.Alpha
}#end of window size loop
nOut=min(maxOut,max(nWin))
index=1:nOut
return(list(FDR=FDR[index,],Power=Power[index,],Power.Alpha=Power.Alpha,alpha=alpha))
}#end of GAPIT.Power
#=============================================================================================
`GAPIT.Power.compare` <-function(myG=NUll,myGD=NULL,myGM=NULL,myKI=NULL,myY=NULL,myCV=NULL,rel=NULL,h2=NULL,NQTN=NULL){
# Object: compare to Power against FDR for GLM,MLM,CMLM,ECMLM,SUPER
# rel:repetition times
# Authors: You Tang
# Last update: December 31, 2014
##############################################################################################
if(is.null(myG)||is.null(myGD)||is.null(myGM)||is.null(myKI)){stop("Read data Invalid. Please select read valid flies !")}
if(is.null(rel))
rel=100
if(is.null(h2))
h2=0.85
if(is.null(NQTN))
NQTN=5
X<-myGD[,-1]
taxa<-myGD[,1]
taxa<-as.character(taxa)
##simulation phyenotype
##-------------------------##
n=nrow(X)
m=ncol(X)
rep.power.GLM<-data.frame(matrix(0,100,6))
rep.FDR.GLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.GLM<-data.frame(matrix(0,12,6))
rep.power.MLM<-data.frame(matrix(0,100,6))
rep.FDR.MLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.MLM<-data.frame(matrix(0,12,6))
rep.power.SUPER<-data.frame(matrix(0,100,6))
rep.FDR.SUPER<-data.frame(matrix(0,100,6))
rep.Power.Alpha.SUPER<-data.frame(matrix(0,12,6))
rep.power.CMLM<-data.frame(matrix(0,100,6))
rep.FDR.CMLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.CMLM<-data.frame(matrix(0,12,6))
rep.power.ECMLM<-data.frame(matrix(0,100,6))
rep.FDR.ECMLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.ECMLM<-data.frame(matrix(0,12,6))
##PCA
##---------------------##
PCA<-prcomp(X)
PCVar<-PCA$sdev^2
myPC<-PCA$x[,1:3]
m1<-as.data.frame(myPC)
myCV<-cbind(taxa,m1)
myCV<-as.data.frame(myCV)
##-----end step 2 for tfam---###
kcv1<-matrix(1,nrow(myCV),1)
kcv<-cbind(data.frame(kcv1),myCV)
write.table(kcv,"pca.txt",row.names = FALSE,col.names = FALSE,sep="\t",quote=FALSE)
for(i in 1:rel)
{
addm<-matrix(rnorm(NQTN,0,1),NQTN,1)
QTN.position<-sample(1:m,NQTN,replace=FALSE)
SNPQ<-as.matrix(X[,QTN.position])
ge<-SNPQ%*%addm
vg<-var(ge)
ve<-vg*(1-h2)/h2
SDE<-sqrt(ve)
res<-rnorm(n,0,SDE)
y=as.data.frame(ge+res)
myY<-cbind(taxa,y)
myY<-as.data.frame(myY)
max.groups=nrow(myY)
print(paste("*****************","GWAS by GAPIT...GLM model",i," totle:",rel,sep=""))
#--------------------------
myGAPIT_GLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
PCA.total=3,
file.output=FALSE,
model="GLM",
memo="GLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("*****************","GWAS by GAPIT...MLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_MLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
file.output=FALSE,
model="MLM",
memo="MLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("*****************","GWAS by GAPIT...SUPER model",i," totle:",rel,sep=""))
##--------------------------------#
myGAPIT_SUPER <- GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
#PCA.total=3,
model="SUPER",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
file.output=FALSE,
)
print(paste("$$$$$$$$$$$$$$$","GWAS by GAPIT...CMLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_CMLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
file.output=FALSE,
model="CMLM",
memo="CMLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("-------------------","GWAS by GAPIT...ECMLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_ECMLM=GAPIT(
Y=myY,
G=myG,
#GD=myGD,
#GM=myGM,
#KI=myKI,
#CV=myCV,
PCA.total=3,
kinship.cluster=c("average", "complete", "ward"),
kinship.group=c("Mean", "Max"),
file.output=FALSE,
model="ECMLM",
memo="ECMLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
power_ecmlm<-GAPIT.Power(WS=c(1e0,1e3,1e4,1e5,1e6,1e7), alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1), maxOut=100,seqQTN=QTN.position,GM=myGM,GWAS=myGAPIT_ECMLM$GWAS)
#power #FDR #Power.Alpha
rep.power.GLM<-rep.power.GLM+myGAPIT_GLM$Power
rep.FDR.GLM<-rep.FDR.GLM+myGAPIT_GLM$FDR
rep.Power.Alpha.GLM<-rep.Power.Alpha.GLM+myGAPIT_GLM$Power.Alpha
rep.power.MLM<-rep.power.MLM+myGAPIT_MLM$Power
rep.FDR.MLM<-rep.FDR.MLM+myGAPIT_MLM$FDR
rep.Power.Alpha.MLM<-rep.Power.Alpha.MLM+myGAPIT_MLM$Power.Alpha
rep.power.SUPER<-rep.power.SUPER+myGAPIT_SUPER$Power
rep.FDR.SUPER<-rep.FDR.SUPER+myGAPIT_SUPER$FDR
rep.Power.Alpha.SUPER<-rep.Power.Alpha.SUPER+myGAPIT_SUPER$Power.Alpha
rep.power.CMLM<-rep.power.CMLM+myGAPIT_CMLM$Power
rep.FDR.CMLM<-rep.FDR.CMLM+myGAPIT_CMLM$FDR
rep.Power.Alpha.CMLM<-rep.Power.Alpha.CMLM+myGAPIT_CMLM$Power.Alpha
rep.power.ECMLM<-rep.power.ECMLM+power_ecmlm$Power
rep.FDR.ECMLM<-rep.FDR.ECMLM+power_ecmlm$FDR
rep.Power.Alpha.ECMLM<-rep.Power.Alpha.ECMLM+power_ecmlm$Power.Alpha
gc()
}
#mean
rep.power.GLM<-rep.power.GLM/rel
rep.FDR.GLM<-rep.FDR.GLM/rel
rep.Power.Alpha.GLM<-rep.Power.Alpha.GLM/rel
rep.power.MLM<-rep.power.MLM/rel
rep.FDR.MLM<-rep.FDR.MLM/rel
rep.Power.Alpha.MLM<-rep.Power.Alpha.MLM/rel
rep.power.SUPER<-rep.power.SUPER/rel
rep.FDR.SUPER<-rep.FDR.SUPER/rel
rep.Power.Alpha.SUPER<-rep.Power.Alpha.SUPER/rel
rep.power.CMLM<-rep.power.CMLM/rel
rep.FDR.CMLM<-rep.FDR.CMLM/rel
rep.Power.Alpha.CMLM<-rep.Power.Alpha.CMLM/rel
rep.power.ECMLM<-rep.power.ECMLM/rel
rep.FDR.ECMLM<-rep.FDR.ECMLM/rel
rep.Power.Alpha.ECMLM<-rep.Power.Alpha.ECMLM/rel
#ouput files power FDR for GLM,MLM,SUPER
myWS=c(1e0,1e3,1e4,1e5,1e6,1e7)
myalpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)
colnames(rep.FDR.GLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.GLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.GLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.MLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.MLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.MLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.SUPER)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.SUPER)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.SUPER)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.CMLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.CMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.CMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.ECMLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.ECMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.ECMLM)=paste("Power(",myWS,")",sep="")
write.csv(cbind(rep.FDR.GLM,rep.power.GLM),paste(h2,"_",NQTN,".Power.by.FDR.GLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.GLM),paste(h2,"_",NQTN,".Power.by.TypeI.GLM",".csv",sep=""))
write.csv(cbind(rep.FDR.MLM,rep.power.MLM),paste(h2,"_",NQTN,".Power.by.FDR.MLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.MLM),paste(h2,"_",NQTN,".Power.by.TypeI.MLM",".csv",sep=""))
write.csv(cbind(rep.FDR.SUPER,rep.power.SUPER),paste(h2,"_",NQTN,".Power.by.FDR.SUPER",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.SUPER),paste(h2,"_",NQTN,".Power.by.TypeI.SUPER",".csv",sep=""))
write.csv(cbind(rep.FDR.CMLM,rep.power.CMLM),paste(h2,"_",NQTN,".Power.by.FDR.CMLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.CMLM),paste(h2,"_",NQTN,".Power.by.TypeI.CMLM",".csv",sep=""))
write.csv(cbind(rep.FDR.ECMLM,rep.power.ECMLM),paste(h2,"_",NQTN,".Power.by.FDR.ECMLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.ECMLM),paste(h2,"_",NQTN,".Power.by.TypeI.ECMLM",".csv",sep=""))
write.csv(cbind(rep.FDR.GLM[,6],rep.power.GLM[,6],rep.FDR.MLM[,6],rep.power.MLM[,6],rep.FDR.CMLM[,6],rep.power.CMLM[,6],rep.FDR.ECMLM[,6],rep.power.ECMLM[,6],rep.FDR.SUPER[,6],rep.power.SUPER[,6]),paste(h2,"_",NQTN,".Power.by.FDR.GLM.MLM.SUPER",rel,".csv",sep=""))
name.of.trait=noquote(names(myY)[2])
pdf(paste("GAPIT.Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER.", ".pdf", sep = ""), width = 4.5, height = 4.5,pointsize=9)
par(mar = c(5,6,5,3))
#win.graph(width=6, height=4, pointsize=9)
#palette(c("blue","red","green4","brown4","orange",rainbow(5)))
palette(c("green4","red","blue","brown4","orange",rainbow(5)))
plot(rep.FDR.SUPER[,6],rep.power.SUPER[,6],bg="lightgray",xlab="FDR",ylab="Power",ylim=c(0,1),xlim=c(0,1),main="Power against FDR",type="o",pch=20,col=1,cex=1.0,cex.lab=1.3, cex.axis=1, lwd=2,las=1)
lines(rep.power.ECMLM[,6]~rep.FDR.ECMLM[,6], lwd=2,type="o",pch=20,col=2)
lines(rep.power.CMLM[,6]~rep.FDR.CMLM[,6], lwd=2,type="o",pch=20,col=3)
lines(rep.power.MLM[,6]~rep.FDR.MLM[,6], lwd=2,type="o",pch=20,col=4)
lines(rep.power.GLM[,6]~rep.FDR.GLM[,6], lwd=2,type="o",pch=20,col=5)
legend("bottomright",c("SUPER","ECMLM","CMLM","MLM","GLM"), pch = 20, lty =1,col=c(1:5),lwd=2,cex=1.0,bty="n")
#
dev.off()
###add type I error and power###
kkt<-cbind(rep.Power.Alpha.SUPER[,1],rep.Power.Alpha.ECMLM[,1],rep.Power.Alpha.CMLM[,1],rep.Power.Alpha.MLM[,1],rep.Power.Alpha.GLM[,1])
write.csv(cbind(myalpha,rep.Power.Alpha.SUPER[,1],rep.Power.Alpha.ECMLM[,1],rep.Power.Alpha.CMLM[,1],rep.Power.Alpha.MLM[,1],rep.Power.Alpha.GLM[,1]),paste(h2,"_",NQTN,".Type I error.Power.by.FDR.GLM.MLM.SUPER",rel,".csv",sep=""))
myalpha1<-myalpha/10
pdf(paste("GAPIT.Type I error_Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER.", ".pdf", sep = ""), width = 6, height = 4.5,pointsize=9)
par(mar = c(5,6,5,3))
#win.graph(width=6, height=4, pointsize=9)
#palette(c("blue","red","green4","brown4","orange",rainbow(5)))
palette(c("green4","red","blue","brown4","orange",rainbow(5)))
plot(myalpha1,rep.Power.Alpha.SUPER[,1],log="x",bg="lightgray",xlab="Type I error",ylab="Power",main="Power against FDR",type="o",pch=20,col=1,cex=1.0,cex.lab=1.3, cex.axis=1, lwd=2,las=1,ylim=c(min(kkt),max(kkt)))
#plot(myalpha1,rep.Power.Alpha.SUPER[,1],bg="lightgray",xlab="Type I error",ylab="Power",ylim=c(0,1),xlim=c(0,1),main="Power against FDR",type="o",pch=20,col=1,cex=1.0,cex.lab=1.3, cex.axis=1, lwd=2,las=1)
lines(rep.Power.Alpha.ECMLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=2)
lines(rep.Power.Alpha.CMLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=3)
lines(rep.Power.Alpha.MLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=4)
lines(rep.Power.Alpha.GLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=5)
legend("bottomright",c("SUPER","ECMLM","CMLM","MLM","GLM"), pch = 20, lty =1,col=c(1:5),lwd=2,cex=1.0,bty="n")
#
dev.off()
print(paste("GAPIT.Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER.","successfully!" ,sep = ""))
#return(list(inf_Y_all,ref_Y_all))
}#end compare to GLM,MLM,CMLM,ECMLM,SUPER
#=============================================================================================
`GAPIT.Power.compare.plink` <-function(myG=null,myGD=NULL,myGM=NULL,myKI=NULL,myY=NULL,myCV=NULL,rel=NULL,h2=NULL,NQTN=NULL){
# Object: compare to Power against FDR for GLM,MLM,CMLM,ECMLM,SUPER,PLINK
# rel:repetition times
# Authors: You Tang
# Last update: January 23, 2015
##############################################################################################
if(is.null(myG)||is.null(myGD)||is.null(myGM)||is.null(myKI)){stop("Read data Invalid. Please select read valid flies !")}
if(is.null(rel))
rel=100
if(is.null(h2))
h2=0.85
if(is.null(NQTN))
NQTN=5
X<-myGD[,-1]
taxa<-myGD[,1]
taxa<-as.character(taxa)
##simulation phyenotype
##-------------------------##
n=nrow(X)
m=ncol(X)
####handle plink tped output work direct####
G<-myG[-1,]
GD<-t(X)
v3<-matrix(0,nrow(G),1)
kk<-cbind(data.frame(G[,3]),data.frame(G[,1]),data.frame(v3),data.frame(G[,4]),GD)
b1<-nrow(kk)
b2<-ncol(kk)
for(i in 1:b1){
for(j in 5:b2){
##imput number 1
if(kk[i,j]==0)
kk[i,j]=1
}
}
kk4<-cbind(kk[,5],kk[,5])
for(j in 6:b2){
kk4<-cbind(data.frame(kk4),data.frame(kk[,j]),data.frame(kk[,j]))
}
kk6<-cbind(kk[,1:4],kk4)
##output plink deal with tped
write.table(data.frame(kk6),"mdp_numeric.tped",row.names = FALSE,col.names = FALSE,sep="\t",quote=FALSE)
################----------end tped for pinlk-------------##########
rep.power.GLM<-data.frame(matrix(0,100,6))
rep.FDR.GLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.GLM<-data.frame(matrix(0,12,6))
rep.power.MLM<-data.frame(matrix(0,100,6))
rep.FDR.MLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.MLM<-data.frame(matrix(0,12,6))
rep.power.SUPER<-data.frame(matrix(0,100,6))
rep.FDR.SUPER<-data.frame(matrix(0,100,6))
rep.Power.Alpha.SUPER<-data.frame(matrix(0,12,6))
rep.power.CMLM<-data.frame(matrix(0,100,6))
rep.FDR.CMLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.CMLM<-data.frame(matrix(0,12,6))
rep.power.ECMLM<-data.frame(matrix(0,100,6))
rep.FDR.ECMLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.ECMLM<-data.frame(matrix(0,12,6))
#####------handle tfam for plink----###
rep.power.plink<-data.frame(matrix(0,100,6))
rep.FDR.plink<-data.frame(matrix(0,100,6))
rep.Power.Alpha.plink<-data.frame(matrix(0,12,6))
k1<-matrix(1,n,1)
k2<-matrix(-9,n,2)
##------step 1 end-----------##
WS=c(1e0,1e3,1e4,1e5,1e6,1e7)
alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)
maxOut=100
##PCA
##---------------------##
PCA<-prcomp(X)
PCVar<-PCA$sdev^2
myPC<-PCA$x[,1:3]
m1<-as.data.frame(myPC)
myCV<-cbind(taxa,m1)
myCV<-as.data.frame(myCV)
##-----end step 2 for tfam---###
kcv1<-matrix(1,nrow(myCV),1)
kcv<-cbind(data.frame(kcv1),myCV)
write.table(kcv,"pca.txt",row.names = FALSE,col.names = FALSE,sep="\t",quote=FALSE)
for(i in 1:rel)
{
addm<-matrix(rnorm(NQTN,0,1),NQTN,1)
QTN.position<-sample(1:m,NQTN,replace=FALSE)
SNPQ<-as.matrix(X[,QTN.position])
ge<-SNPQ%*%addm
vg<-var(ge)
ve<-vg*(1-h2)/h2
SDE<-sqrt(ve)
res<-rnorm(n,0,SDE)
y=as.data.frame(ge+res)
myY<-cbind(taxa,y)
myY<-as.data.frame(myY)
##-----output tfam for plink----##
k3<-cbind(data.frame(k1),data.frame(taxa),data.frame(k2),data.frame(k1),data.frame(myY[,2]))
write.table(k3,paste("mdp_numeric",i,".tfam",sep=""),row.names = FALSE,col.names = FALSE,sep="\t",quote=FALSE)
##-----end step 2 for tfam---###
max.groups=nrow(y)
print(paste("*****************","GWAS by GAPIT...GLM model",i," totle:",rel,sep=""))
#--------------------------
myGAPIT_GLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
PCA.total=3,
file.output=FALSE,
group.from=0,
group.to=0,
group.by=0,
memo="GLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("*****************","GWAS by GAPIT...MLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_MLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
file.output=FALSE,
group.from=max.groups,
group.to=max.groups,
group.by=10,
memo="MLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("*****************","GWAS by GAPIT...SUPER model",i," totle:",rel,sep=""))
##--------------------------------#
myGAPIT_SUPER <- GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
#PCA.total=3,
sangwich.top="MLM", #options are GLM,MLM,CMLM, FaST and SUPER
sangwich.bottom="SUPER", #options are GLM,MLM,CMLM, FaST and SUPER
LD=0.1,
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
file.output=FALSE,
)
print(paste("$$$$$$$$$$$$$$$","GWAS by GAPIT...CMLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_CMLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
file.output=FALSE,
group.from=0,
group.to=max.groups,
group.by=10,
memo="CMLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("-------------------","GWAS by GAPIT...ECMLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_ECMLM=GAPIT(
Y=myY,
G=myG,
#GD=myGD,
#GM=myGM,
#KI=myKI,
#CV=myCV,
PCA.total=3,
kinship.cluster=c("average", "complete", "ward"),
kinship.group=c("Mean", "Max"),
file.output=FALSE,
group.from=0,
group.to=max.groups,
group.by=10,
memo="ECMLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
##ecmlm power
power_ecmlm<-GAPIT.Power(WS=WS, alpha=alpha, maxOut=maxOut,seqQTN=QTN.position,GM=myGM,GWAS=myGAPIT_ECMLM$GWAS)
##-------------GAWS for plink-----##
##---output gwas.mdp_numericx.qassoc by plink.exe,so must be copy it to work path!----##
system(paste('"plink.exe"', paste('--tped mdp_numeric.tped --tfam mdp_numeric',i,'.tfam --assoc --out gwas.mdp_numeric',i,sep='')), wait = TRUE)
##-------------GAWS for plink-----##
##---output gwas.mdp_numericx.qassoc by plink.exe,so must be copy it to work path!----##
system(paste('"plink.exe"', paste('--tped mdp_numeric.tped --tfam mdp_numeric',i,'.tfam --covar pca.txt --linear --hide-covar --out gwas.mdp_numeric',i,sep='')), wait = TRUE)
plinkGWAS<-read.table(paste("gwas.mdp_numeric",i,".assoc.linear",sep=""),header=T)
Format_GWAS=cbind(myGM,plinkGWAS[,9],rep(NA,nrow(myGM)),rep(NA,nrow(myGM)),rep(NA,nrow(myGM)))
names(Format_GWAS)<-c("SNP","Chromosome","Position","P.value","maf","nobs","FDR_Adjusted_P-values")
power_plink<-GAPIT.Power(WS=WS, alpha=alpha, maxOut=maxOut,seqQTN=QTN.position,GM=myGM,GWAS=Format_GWAS)
##---end powe_plink-----###
##----end step 3 for plink----###
#power #FDR #Power.Alpha
rep.power.GLM<-rep.power.GLM+myGAPIT_GLM$Power
rep.FDR.GLM<-rep.FDR.GLM+myGAPIT_GLM$FDR
rep.Power.Alpha.GLM<-rep.Power.Alpha.GLM+myGAPIT_GLM$Power.Alpha
rep.power.MLM<-rep.power.MLM+myGAPIT_MLM$Power
rep.FDR.MLM<-rep.FDR.MLM+myGAPIT_MLM$FDR
rep.Power.Alpha.MLM<-rep.Power.Alpha.MLM+myGAPIT_MLM$Power.Alpha
rep.power.SUPER<-rep.power.SUPER+myGAPIT_SUPER$Power
rep.FDR.SUPER<-rep.FDR.SUPER+myGAPIT_SUPER$FDR
rep.Power.Alpha.SUPER<-rep.Power.Alpha.SUPER+myGAPIT_SUPER$Power.Alpha
rep.power.CMLM<-rep.power.CMLM+myGAPIT_CMLM$Power
rep.FDR.CMLM<-rep.FDR.CMLM+myGAPIT_CMLM$FDR
rep.Power.Alpha.CMLM<-rep.Power.Alpha.CMLM+myGAPIT_CMLM$Power.Alpha
rep.power.ECMLM<-rep.power.ECMLM+power_ecmlm$Power
rep.FDR.ECMLM<-rep.FDR.ECMLM+power_ecmlm$FDR
rep.Power.Alpha.ECMLM<-rep.Power.Alpha.ECMLM+power_ecmlm$Power.Alpha
##----power-fdr save for mean of plink---##
rep.power.plink<-rep.power.plink+power_plink$Power
rep.FDR.plink<-rep.FDR.plink+power_plink$FDR
rep.Power.Alpha.plink<-rep.Power.Alpha.plink+power_plink$Power.Alpha
##---end sum for power of plink ----##
gc()
}
#mean
rep.power.GLM<-rep.power.GLM/rel
rep.FDR.GLM<-rep.FDR.GLM/rel
rep.Power.Alpha.GLM<-rep.Power.Alpha.GLM/rel
rep.power.MLM<-rep.power.MLM/rel
rep.FDR.MLM<-rep.FDR.MLM/rel
rep.Power.Alpha.MLM<-rep.Power.Alpha.MLM/rel
rep.power.SUPER<-rep.power.SUPER/rel
rep.FDR.SUPER<-rep.FDR.SUPER/rel
rep.Power.Alpha.SUPER<-rep.Power.Alpha.SUPER/rel
rep.power.CMLM<-rep.power.CMLM/rel
rep.FDR.CMLM<-rep.FDR.CMLM/rel
rep.Power.Alpha.CMLM<-rep.Power.Alpha.CMLM/rel
rep.power.ECMLM<-rep.power.ECMLM/rel
rep.FDR.ECMLM<-rep.FDR.ECMLM/rel
rep.Power.Alpha.ECMLM<-rep.Power.Alpha.ECMLM/rel
rep.power.plink<-rep.power.plink/rel
rep.FDR.plink<-rep.FDR.plink/rel
rep.Power.Alpha.plink<-rep.Power.Alpha.plink/rel
#ouput files power FDR for GLM,MLM,SUPER
myWS=c(1e0,1e3,1e4,1e5,1e6,1e7)
myalpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)
colnames(rep.FDR.GLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.GLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.GLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.MLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.MLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.MLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.SUPER)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.SUPER)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.SUPER)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.CMLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.CMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.CMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.ECMLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.ECMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.ECMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.plink)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.plink)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.plink)=paste("Power(",myWS,")",sep="")
write.csv(cbind(rep.FDR.GLM,rep.power.GLM),paste(h2,"_",NQTN,".Power.by.FDR.GLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.GLM),paste(h2,"_",NQTN,".Power.by.TypeI.GLM",".csv",sep=""))
write.csv(cbind(rep.FDR.MLM,rep.power.MLM),paste(h2,"_",NQTN,".Power.by.FDR.MLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.MLM),paste(h2,"_",NQTN,".Power.by.TypeI.MLM",".csv",sep=""))
write.csv(cbind(rep.FDR.SUPER,rep.power.SUPER),paste(h2,"_",NQTN,".Power.by.FDR.SUPER",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.SUPER),paste(h2,"_",NQTN,".Power.by.TypeI.SUPER",".csv",sep=""))
write.csv(cbind(rep.FDR.CMLM,rep.power.CMLM),paste(h2,"_",NQTN,".Power.by.FDR.CMLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.CMLM),paste(h2,"_",NQTN,".Power.by.TypeI.CMLM",".csv",sep=""))
write.csv(cbind(rep.FDR.ECMLM,rep.power.ECMLM),paste(h2,"_",NQTN,".Power.by.FDR.ECMLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.ECMLM),paste(h2,"_",NQTN,".Power.by.TypeI.ECMLM",".csv",sep=""))
write.csv(cbind(rep.FDR.plink,rep.power.plink),paste(h2,"_",NQTN,".Power.by.FDR.plink",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.plink),paste(h2,"_",NQTN,".Power.by.TypeI.plink",".csv",sep=""))
write.csv(cbind(rep.FDR.GLM[,6],rep.power.GLM[,6],rep.FDR.MLM[,6],rep.power.MLM[,6],rep.FDR.CMLM[,6],rep.power.CMLM[,6],rep.FDR.ECMLM[,6],rep.power.ECMLM[,6],rep.FDR.SUPER[,6],rep.power.SUPER[,6],rep.FDR.plink[,6],rep.power.plink[,6]),paste(h2,"_",NQTN,".Power.by.FDR.GLM.MLM.SUPER.plink",rel,".csv",sep=""))
name.of.trait=noquote(names(myY)[2])
pdf(paste("GAPIT.Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER.plink", ".pdf", sep = ""), width = 4.5, height = 4,pointsize=9)
par(mar = c(5,6,5,3))
#win.graph(width=6, height=4, pointsize=9)
palette(c("green4","red","blue","brown4","orange","black",rainbow(6)))
plot(rep.FDR.SUPER[,6],rep.power.SUPER[,6],bg="lightgray",xlab="FDR",ylab="Power",ylim=c(0,1),xlim=c(0,1),main="Power against FDR",type="o",pch=20,col=1,cex=1.0,cex.lab=1.3, cex.axis=1, lwd=2,las=1)
lines(rep.power.ECMLM[,6]~rep.FDR.ECMLM[,6], lwd=2,type="o",pch=20,col=2)
lines(rep.power.CMLM[,6]~rep.FDR.CMLM[,6], lwd=2,type="o",pch=20,col=3)
lines(rep.power.MLM[,6]~rep.FDR.MLM[,6], lwd=2,type="o",pch=20,col=4)
lines(rep.power.GLM[,6]~rep.FDR.GLM[,6], lwd=2,type="o",pch=20,col=5)
lines(rep.power.plink[,6]~rep.FDR.plink[,6], lwd=2,type="o",pch=20,col=6,lty =1)
legend("bottomright",c("SUPER","ECMLM","CMLM","MLM","GLM","PLINK"), pch =c(20,20,20,20,20,20), lty =c(1,1,1,1,1,2),col=c(1:6),lwd=2,cex=1.0,bty="n")
#
dev.off()
###add type I error and power###
kkt<-cbind(rep.Power.Alpha.SUPER[,1],rep.Power.Alpha.ECMLM[,1],rep.Power.Alpha.CMLM[,1],rep.Power.Alpha.MLM[,1],rep.Power.Alpha.GLM[,1],rep.Power.Alpha.plink[,1])
write.csv(cbind(myalpha,rep.Power.Alpha.SUPER[,1],rep.Power.Alpha.ECMLM[,1],rep.Power.Alpha.CMLM[,1],rep.Power.Alpha.MLM[,1],rep.Power.Alpha.GLM[,1],rep.Power.Alpha.plink[,1]),paste(h2,"_",NQTN,".Type I error.Power.by.FDR.GLM.MLM.SUPER",rel,".csv",sep=""))
myalpha1<-myalpha/10
pdf(paste("GAPIT.Type I error_Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER,plink", ".pdf", sep = ""), width = 6, height = 4.5,pointsize=9)
par(mar = c(5,6,5,3))
palette(c("green4","red","blue","brown4","orange","black",rainbow(6)))
plot(myalpha1,rep.Power.Alpha.SUPER[,1],log="x",bg="lightgray",xlab="Type I error",ylab="Power",main="Power against FDR",type="o",pch=20,col=1,cex=1.0,cex.lab=1.3, cex.axis=1, lwd=2,las=1,ylim=c(min(kkt),max(kkt)))
lines(rep.Power.Alpha.ECMLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=2)
lines(rep.Power.Alpha.CMLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=3)
lines(rep.Power.Alpha.MLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=4)
lines(rep.Power.Alpha.GLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=5)
lines(rep.Power.Alpha.plink[,1]~myalpha1, lwd=2,type="o",pch=20,col=6,lty =1)
legend("bottomright",c("SUPER","ECMLM","CMLM","MLM","GLM","PLINK"), pch =c(20,20,20,20,20,20), lty =c(1,1,1,1,1,2),col=c(1:6),lwd=2,cex=1.0,bty="n")
dev.off()
print(paste("GAPIT.Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER,PLINK.","successfully!" ,sep = ""))
#return(list(inf_Y_all,ref_Y_all))
}#end compare to GLM,MLM,SUPER
#=============================================================================================
`GAPIT.Prediction` <-function(myK=NULL,y=NULL, num=NULL){
# Object: Genetic Prediction one time by cross validation and cMLM,result:a pdf of the scree plot
# myK:Kinship
# Y: phenotype with columns of taxa,Y1,Y2...
# num:folders number
# Authors: Jiabo Wang and You Tang
# Last update: December 31, 2014
##############################################################################################
if(is.null(myK)||is.null(y)){stop("Validation Invalid. Please select read valid flies !")}
if(is.null(num))
{
num=5 #not input num value,default folders number is 5
}
y=y[,1:2]
m=nrow(y)
m.sample=round(m/num)
if(num<2||num>m){stop("Validation Invalid. Please select folders num >1 !")}
vali<-matrix(nr=m.sample,nc=num-1)
cali<-matrix(nr=m-m.sample,nc=num-1)
#vali<-list(v1=unique(as.character(sample(y$Taxa, m.sample))))
#cali<-list(c1=y[!(y$Taxa %in% as.matrix(as.data.frame(vali[1]))), 'Taxa'])
vali[,1]<-unique(as.character(sample(y$Taxa, m.sample)))
cali[,1]<-unique(as.character(y[!(y$Taxa %in% vali[,1]), 'Taxa']))
for(j in 2:num)
{
if(j!=num)
{
vali[,j]<-unique(as.character(sample(y[!(y$Taxa %in% vali[,1:j-1]), 'Taxa'], m.sample) ))
}
if(j==num)
{
valilast=unique(as.character(y[!(y$Taxa %in% vali[,1:j-1]), 'Taxa']))
}
if(j!=num)
cali[,j]<-unique(as.character(y[!(y$Taxa %in% vali[,j]), 'Taxa']))
if(j==num)
calilast <<- y[!(y$Taxa %in% valilast), 'Taxa']
}
i=sample(1:num, size = 1)
if(i!=num){
lines.vali<-vali[,i]
}else{
lines.vali<-valilast
}
#use only genotypes that were genotyped and phenotyped
commonGeno_v <- lines.vali[lines.vali %in% myK[,1]]
yvali<- y[match(commonGeno_v,y$Taxa),]
if(i!=num){
lines.cali<-cali[,i]
}else{
lines.cali<-calilast
}
#use only genotypes that were genotyped and phenotyped
commonGeno_c <- lines.cali[lines.cali %in% myK[,1]]
ycali<- y[match(commonGeno_c,y$Taxa),]
Y.raw=ycali[,c(1,2)]#choos a trait
myY=Y.raw
myKI=myK
max.groups=m
#Run GAPIT
#############################################
blupGAPIT <- GAPIT(
Y=myY,
KI=myKI,
#group.from=max.groups,
group.from=1,
group.to=max.groups,
#group.by=10,
#PCA.total=3,
SNP.test=FALSE,
file.output=FALSE
)
blup_prediction=blupGAPIT$GPS
blue<-blupGAPIT$Pred$BLUE
mean_blue<-mean(blue)
blup_prediction.ref<-blup_prediction[match(commonGeno_c,blup_prediction$Taxa),]
blup_prediction.inf<-blup_prediction[match(commonGeno_v,blup_prediction$Taxa),]
inf_BLUP<-blup_prediction.inf$BLUP
ref_BLUP<-blup_prediction.ref$BLUP
inf_pred<-inf_BLUP+mean_blue
ref_pred<-ref_BLUP+mean_blue
inf_all<-cbind(blup_prediction.inf,inf_pred)
ref_all<-cbind(blup_prediction.ref,ref_pred)
inf_Y_all<-merge(y,inf_all,by.x="Taxa",by.y="Taxa")
ref_Y_all<-merge(y,ref_all,by.x="Taxa",by.y="Taxa")
name.of.trait=noquote(names(Y.raw)[2])
pdf(paste("GAPIT.Prediction ", name.of.trait,".Predict reference.pdf", sep = ""), width =6, height = 6)
par(mar = c(5,5,5,5))
plot(ref_Y_all[,2],ref_Y_all[,8],pch=1,xlab="Observed(Ref)",ylab="Predicted(Ref)",cex.lab=1.3,cex.axis=1.2,lwd=2) #xlim=c(50,110),ylim=c(50,110),
kr<-lm(ref_Y_all[,8]~ref_Y_all[,2])
abline(a = kr$coefficients[1], b = kr$coefficients[2], col = "red",lwd=4,lty=1)
#v1<-max(ref_Y_all[,2]])*10/10
#text(v1,kr$coefficients[1]+kr$coefficients[2]*v1,paste("R^2=",format(kr$coefficients[2], digits = 3),seq=""), col = "blue", adj = c(0, -.1))
legend("bottomright",paste("R^2=",format(kr$coefficients[2], digits = 4),seq=""), col="white",text.col="blue",lwd=2,cex=1.2,bty="n")
dev.off()
pdf(paste("GAPIT.Prediction ", name.of.trait,".Predict inference.pdf", sep = ""), width = 6, height = 6)
par(mar = c(5,5,5,5))
plot(inf_Y_all[,2],inf_Y_all[,8],pch=1,xlab="Observed(Inf)",ylab="Predicted(Inf)",cex.lab=1.5,lwd=2,,cex.axis=1.2)#xlim=c(50,110),ylim=c(45,100),
ki<-lm(inf_Y_all[,8]~inf_Y_all[,2])
abline(a = ki$coefficients[1], b = ki$coefficients[2], col = "red",lwd=3,lty=1)
#v0<-max(inf_Y_all[,2])
#text(v0,ki$coefficients[1]+ki$coefficients[2]*v0,paste("R^2=",format(ki$coefficients[2], digits = 4),seq=""), col = "blue", adj = c(0, -.1))
legend("bottomright",paste("R^2=",format(ki$coefficients[2], digits = 4),seq=""), col="white",text.col="blue",lwd=2,cex=1.2,bty="n")
dev.off()
print(paste("GAPIT.Prediction ", name.of.trait,".Predict phenotype.","successfully!" ,sep = ""))
return(list(inf_Y_all,ref_Y_all))
}
#end Prediction one time
#=============================================================================================
`GAPIT.Pruning` <-
function(values,DPP=5000){
#Object: To get index of subset that evenly distribute
#Output: Index
#Authors: Zhiwu Zhang
# Last update: May 28, 2011
##############################################################################################
#No change if below the requirement
if(length(values)<=DPP)return(c(1:length(values)))
#values= log.P.values
values=sqrt(values) #This shift the weight a little bit to the low building.
#Handler of bias plot
rv=runif(length(values))
values=values+rv
values=values[order(values,decreasing = T)]
theMin=min(values)
theMax=max(values)
range=theMax-theMin
interval=range/DPP
ladder=round(values/interval)
ladder2=c(ladder[-1],0)
keep=ladder-ladder2
index=which(keep>0)
return(index)
}#end of GAPIT.Pruning
#=============================================================================================
`GAPIT.QC` <-
function(Y=NULL,KI=NULL,GT=NULL,CV=NULL,Z=NULL,GK=NULL){
#Object: to do data quality control
#Output: Y, KI, GD, CV, Z, flag
#Authors: Zhiwu Zhang and Alex Lipka
# Last update: April 14, 2011
##############################################################################################
#Remove duplicates
print("Removing duplicates...")
#print(dim(CV))
Y=GAPIT.RemoveDuplicate(Y)
CV=GAPIT.RemoveDuplicate(CV)
GK=GAPIT.RemoveDuplicate(GK)
if(!is.null(Z))Z=GAPIT.RemoveDuplicate(Z)
#Remove missing phenotype
print("Removing NaN...")
Y=Y[which(Y[,2]!="NaN"),]
# Remove duplicates for GT
# GT row wise, Z column wise, and KI both direction.
print("Remove duplicates for GT...")
#print(dim(GT))
if(!is.null(GT))
{
if(is.null(dim(GT)))taxa.kept=unique(GT)
if(!is.null(dim(GT)))taxa.kept=unique(GT[,1])
}else{
taxa.kept=unique(Y[,1])
}
# Remove duplicates for KI
print("Remove duplicates for KI...")
# improve speed: remove t() and use cbind
if(!is.null(KI))
{
taxa.all=KI[,1]
taxa.uniqe=unique(taxa.all)
position=match(taxa.uniqe, taxa.all,nomatch = 0)
position.addition=cbind(1,t(1+position))
KI=KI[position,position.addition]
}
#Sort KI
if(!is.null(KI))
{
taxa.all=KI[,1]
position=order(taxa.all)
position.addition=cbind(1,t(1+position))
KI=KI[position,position.addition]
}
# Remove duplicates for Z rowwise
print("Remove duplicates for Z (column wise)...")
if(!is.null(Z))
{
taxa.all=as.matrix(Z[1,])
taxa.uniqe=intersect(taxa.all,taxa.all)
position=match(taxa.uniqe, taxa.all,nomatch = 0)
Z=Z[,position]
}
#Remove the columns of Z if they are not in KI/GT. KI/GT are allowed to have individuals not in Z
print("Maching Z with Kinship colwise...")
if(!is.null(KI))
{
taxa.all=KI[,1]
taxa.kinship=unique(taxa.all)
}
if(!is.null(Z) & !is.null(KI))
{
#get common taxe between KI and Z
taxa.Z=as.matrix(Z[1,])
#taxa.Z=colnames(Z) #This does not work for names starting with numerical or "-" \
if(is.null(KI)){
taxa.Z_K_common=taxa.Z
}else{
taxa.Z_K_common=intersect(taxa.kinship,taxa.Z)
}
Z <-cbind(Z[,1], Z[,match(taxa.Z_K_common, taxa.Z, nomatch = 0)])
#Remove the rows of Z if all the ellements sum to 0
#@@@ improve speed: too many Zs
print("Maching Z without origin...")
Z1=Z[-1,-1]
Z2=data.frame(Z1)
Z3=as.matrix(Z2)
Z4=as.numeric(Z3) #one dimemtion
Z5=matrix(data = Z4, nrow = nrow(Z1), ncol = ncol(Z1))
RS=rowSums(Z5)>0
#The above process could be simplified!
Z <- Z[c(TRUE,RS),]
#make individuals the same in Z, Y, GT and CV
print("Maching GT and CV...")
if(length(Z)<=1)stop("GAPIT says: there is no place to match IDs!")
}# end of if(!is.null(Z) & !is.null(K))
# get intersect of all the data
taxa=intersect(Y[,1],Y[,1])
if(!is.null(Z))taxa=intersect(Z[-1,1],taxa)
if(!is.null(GT))taxa=intersect(taxa,taxa.kept)
if(!is.null(CV))taxa=intersect(taxa,CV[,1])
if(!is.null(GK))taxa=intersect(taxa,GK[,1])
if(length(taxa)<=1)stop("GAPIT says: There is no individual ID matched to covariate. Please check!")
if(!is.null(Z))
{
#Remove taxa in Z that are not in others, columnwise
t=c(TRUE, Z[-1,1]%in%taxa)
if(length(t)<=2)stop("GAPIT says: There is no individual ID matched among data. Please check!")
Z <- Z[t,]
#Remove the columns of Z if all the ellements sum to 0
print("QC final process...")
#@@@ improve speed: too many Zs
Z1=Z[-1,-1]
Z2=data.frame(Z1)
Z3=as.matrix(Z2)
Z4=as.numeric(Z3) #one dimemtion
Z5=matrix(data = Z4, nrow = nrow(Z1), ncol = ncol(Z1))
CS=colSums(Z5)>0
#The above process could be simplified!
Z <- Z[,c(TRUE,CS)]
}
#Filtering with comman taxa
Y <- Y[Y[,1]%in%taxa,]
if(!is.null(CV)) CV=CV[CV[,1]%in%taxa,]
if(!is.null(GK)) GK=GK[GK[,1]%in%taxa,]
if(!is.null(GT)) taxa.kept=data.frame(taxa.kept[taxa.kept%in%taxa])
#Y <- Y[Y[,1]%in%taxa.kept,]
#To sort Y, GT, CV and Z
Y=Y[order(Y[,1]),]
CV=CV[order(CV[,1]),]
if(!is.null(GK))GK=GK[order(GK[,1]),]
if(!is.null(Z))Z=Z[c(1,1+order(Z[-1,1])),]
#get position of taxa.kept in GT
#position=match(taxa.kept[,1], GT[,1],nomatch = 0)
if(is.null(dim(GT)))position=match(taxa.kept, GT,nomatch = 0)
if(!is.null(dim(GT)))position=match(taxa.kept[,1], GT[,1],nomatch = 0)
if(is.null(dim(taxa.kept)))order.taxa.kept=order(taxa.kept)
if(!is.null(dim(taxa.kept)))order.taxa.kept=order(taxa.kept[,1])
GTindex=position[order.taxa.kept]
flag=nrow(Y)==nrow(Z)-1&nrow(Y)==nrow(GT)&nrow(Y)==nrow(CV)
print("GAPIT.QC accomplished successfully!")
#print(dim(Y))
#print(dim(CV))
#print(dim(KI))
return(list(Y = Y, KI = KI, GT = GT, CV = CV, Z = Z, GK = GK, GTindex=GTindex, flag=flag))
}#The function GAPIT.QC ends here
#=============================================================================================
`GAPIT.QQ` <-
function(P.values, plot.type = "log_P_values", name.of.trait = "Trait",DPP=50000,plot.style="rainbow"){
#Object: Make a QQ-Plot of the P-values
#Options for plot.type = "log_P_values" and "P_values"
#Output: A pdf of the QQ-plot
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: May 9, 2011
##############################################################################################
# Sort the data by the raw P-values
#print("Sorting p values")
#print(paste("Number of P values: ",length(P.values)))
#remove NAs and keep the ones between between 0 and 1
P.values=P.values[!is.na(P.values)]
P.values=P.values[P.values>0]
P.values=P.values[P.values<=1]
if(length(P.values[P.values>0])<1) return(NULL)
N=length(P.values)
DPP=round(DPP/4) #Reduce to 1/4 for QQ plot
P.values <- P.values[order(P.values)]
#Set up the p-value quantiles
#print("Setting p_value_quantiles...")
p_value_quantiles <- (1:length(P.values))/(length(P.values)+1)
if(plot.type == "log_P_values")
{
log.P.values <- -log10(P.values)
log.Quantiles <- -log10(p_value_quantiles)
index=GAPIT.Pruning(log.P.values,DPP=DPP)
log.P.values=log.P.values[index ]
log.Quantiles=log.Quantiles[index]
if(plot.style=="FarmCPU"){
pdf(paste("FarmCPU.", name.of.trait,".QQ-Plot.pdf" ,sep = ""),width = 5,height=5)
par(mar = c(5,6,5,3))
}
if(plot.style=="rainbow"){
pdf(paste("GAPIT.", name.of.trait,".QQ-Plot.pdf" ,sep = ""),width = 5,height=5)
par(mar = c(5,6,5,3))
}
#Add conficence interval
N1=length(log.Quantiles)
## create the confidence intervals
c95 <- rep(NA,N1)
c05 <- rep(NA,N1)
for(j in 1:N1){
i=ceiling((10^-log.Quantiles[j])*N)
if(i==0)i=1
c95[j] <- qbeta(0.95,i,N-i+1)
c05[j] <- qbeta(0.05,i,N-i+1)
#print(c(j,i,c95[j],c05[j]))
}
#CI Lines
#plot(log.Quantiles, -log10(c05), xlim = c(0,max(log.Quantiles)), ylim = c(0,max(log.P.values)), type="l",lty=5, axes=FALSE, xlab="", ylab="",col="black")
#par(new=T)
#plot(log.Quantiles, -log10(c95), xlim = c(0,max(log.Quantiles)), ylim = c(0,max(log.P.values)), type="l",lty=5, axes=FALSE, xlab="", ylab="",col="black")
#CI shade
plot(NULL, xlim = c(0,max(log.Quantiles)), ylim = c(0,max(log.P.values)), type="l",lty=5, lwd = 2, axes=FALSE, xlab="", ylab="",col="gray")
index=length(c95):1
polygon(c(log.Quantiles[index],log.Quantiles),c(-log10(c05)[index],-log10(c95)),col='gray',border=NA)
#Diagonal line
abline(a = 0, b = 1, col = "red",lwd=2)
#data
par(new=T)
if(plot.style=="FarmCPU"){
plot(log.Quantiles, log.P.values, cex.axis=1.1, cex.lab=1.3, lty = 1, lwd = 2, col = "Black" ,bty='l', xlab =expression(Expected~~-log[10](italic(p))), ylab = expression(Observed~~-log[10](italic(p))), main = paste(name.of.trait,sep=""),pch=20)
}
if(plot.style=="rainbow"){
plot(log.Quantiles, log.P.values, xlim = c(0,max(log.Quantiles)), ylim = c(0,max(log.P.values)), cex.axis=1.1, cex.lab=1.3, lty = 1, lwd = 2, col = "Blue" ,xlab =expression(Expected~~-log[10](italic(p))),ylab = expression(Observed~~-log[10](italic(p))), main = paste(name.of.trait,sep=""))
}
dev.off()
}
if(plot.type == "P_values")
{
pdf(paste("QQ-Plot_", name.of.trait,".pdf" ,sep = ""))
par(mar = c(5,5,5,5))
qqplot(p_value_quantiles, P.values, xlim = c(0,1),
ylim = c(0,1), type = "l" , xlab = "Uniform[0,1] Theoretical Quantiles",
lty = 1, lwd = 1, ylab = "Quantiles of P-values from GWAS", col = "Blue",
main = paste(name.of.trait,sep=" "))
abline(a = 0, b = 1, col = "red")
dev.off()
}
#print("GAPIT.QQ accomplished successfully!")
}
#=============================================================================================
`GAPIT` <-
function(Y=NULL,G=NULL,GD=NULL,GM=NULL,KI=NULL,Z=NULL,CV=NULL,CV.Inheritance=NULL,GP=NULL,GK=NULL,
group.from=1000000 ,group.to=1000000,group.by=20,DPP=100000,
kinship.cluster="average", kinship.group='Mean',kinship.algorithm="VanRaden",
bin.from=10000,bin.to=10000,bin.by=10000,inclosure.from=10,inclosure.to=10,inclosure.by=10,
SNP.P3D=TRUE,SNP.effect="Add",SNP.impute="Middle",PCA.total=0, SNP.fraction = 1, seed = NULL, BINS = 20,SNP.test=TRUE,
SNP.MAF=0,FDR.Rate = 1, SNP.FDR=1,SNP.permutation=FALSE,SNP.CV=NULL,SNP.robust="GLM",
file.from=1, file.to=1, file.total=NULL, file.fragment = 99999,file.path=NULL,
file.G=NULL, file.Ext.G=NULL,file.GD=NULL, file.GM=NULL, file.Ext.GD=NULL,file.Ext.GM=NULL,
ngrid = 100, llim = -10, ulim = 10, esp = 1e-10,LD.chromosome=NULL,LD.location=NULL,LD.range=NULL,PCA.col=NULL,PCA.3d=FALSE,NJtree.group=NULL,NJtree.type=c("fan","unrooted"),
sangwich.top=NULL,sangwich.bottom=NULL,QC=TRUE,GTindex=NULL,LD=0.1,plot.bin=10^5,
file.output=TRUE,cutOff=0.01, Model.selection = FALSE,output.numerical = FALSE,
output.hapmap = FALSE, Create.indicator = FALSE,Multi_iter=TRUE,windowsize=5e9,
QTN=NULL, QTN.round=1,QTN.limit=0, QTN.update=TRUE, QTN.method="Penalty", Major.allele.zero = FALSE,
method.GLM="FarmCPU.LM",method.sub="reward",method.sub.final="reward",method.bin="static",bin.size=c(1000000),bin.selection=c(10,20,50,100,200,500,1000),
memo=NULL,Prior=NULL,ncpus=1,maxLoop=3,threshold.output=.01,Inter.Plot=FALSE,Inter.type=c("m","q"),
WS=c(1e0,1e3,1e4,1e5,1e6,1e7),alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),maxOut=100,QTN.position=NULL,CG=NULL,
converge=1,iteration.output=FALSE,acceleration=0,iteration.method="accum",PCA.View.output=TRUE,Geno.View.output=TRUE,plot.style="Oceanic",SUPER_GD=NULL,SUPER_GS=FALSE,
h2=NULL,NQTN=NULL,QTNDist="normal",effectunit=1,category=1,r=0.25,cveff=NULL,a2=0,adim=2,Multiple_analysis=FALSE,
model="MLM",Para=NULL
){
#Object: To perform GWAS and GPS (Genomic Prediction/Selection)
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("--------------------- Welcome to GAPIT ----------------------------")
echo=TRUE
GAPIT.Version=GAPIT.0000()
#
if(!is.null(model))if(!match(model,c("MLM","CMLM","SUPER","GLM","FarmCPU","Blink","MLMM","gBLUP","cBLUP","sBLUP"))) stop(paste("PLease choose one model from ","MLM","CMLM","SUPER","GLM","FarmCPU","Blink","gBLUP","cBLUP","sBLUP",sep=""))
#Allow either KI or K, but not both
if(model%in%c("gBLUP","cBLUP","sBLUP"))
{
SNP.test=FALSE
SUPER_GS=TRUE
}
if(!is.null(KI)&is.null(GD)&is.null(G)&is.null(file.G)&is.null(file.GD))SNP.test=FALSE
model_store=model
for(m in 1:length(model_store))
{
model=model_store[m]
if(!is.null(Y))
{
if(group.from<nrow(Y)) model="CMLM"
}
if(group.to!=group.from)model="CMLM"
if(group.to==1&group.from==1)model="GLM"
if(!is.null(sangwich.bottom)&!is.null(sangwich.bottom))model="SUPER"
if(model=="gBLUP") model="MLM"
if(model=="cBLUP") model="CMLM"
if(model=="sBLUP")
{ model="MLM"
if(!is.null(inclosure.from)&is.null(Para$inclosure.from))Para$inclosure.from=inclosure.from
if(is.null(Para$inclosure.from))Para$inclosure.from=10
if(!is.null(inclosure.to)&is.null(Para$inclosure.to))Para$inclosure.to=inclosure.to
if(is.null(Para$inclosure.to))Para$inclosure.to=100
if(!is.null(inclosure.by)&is.null(Para$inclosure.by))Para$inclosure.by=inclosure.by
if(is.null(Para$inclosure.by))Para$inclosure.by=10
if(!is.null(bin.from)&is.null(Para$bin.from))Para$bin.from=bin.from
if(is.null(Para$bin.from))Para$bin.from=10000
if(!is.null(bin.to)&is.null(Para$bin.to))Para$bin.to=bin.to
if(is.null(Para$bin.to))Para$bin.to=10000
if(!is.null(bin.by)&is.null(Para$bin.by))Para$bin.by=bin.by
if(is.null(Para$bin.by))Para$bin.by=10000
if(!is.null(sangwich.top)&is.null(Para$sangwich.top))Para$sangwich.top=sangwich.top
if(is.null(Para$sangwich.top))Para$sangwich.top="MLM"
if(!is.null(sangwich.bottom)&is.null(Para$sangwich.bottom))Para$sangwich.bottom=sangwich.bottom
if(is.null(Para$sangwich.bottom))Para$sangwich.bottom="SUPER"
}
#CMLM
if(model=="GLM")
{
Para$group.from=1
Para$group.to=1
Para$group.by=10
}
if(model=="MLM")
{
Para$group.from=1000000
Para$group.to=1000000
Para$group.by=10
}
if(model=="CMLM")
{
if(is.null(Para$group.from))Para$group.from=group.from
if(is.null(Para$group.to))Para$group.to=group.to
if(is.null(Para$group.by))Para$group.by=group.by
if(Para$group.from==Para$group.to)Para$group.from=10
if(is.null(Para$group.by))Para$group.by=30
}
if(model=="SUPER")
{
if(!is.null(inclosure.from)&is.null(Para$inclosure.from))Para$inclosure.from=inclosure.from
if(is.null(Para$inclosure.from))Para$inclosure.from=10
if(!is.null(inclosure.to)&is.null(Para$inclosure.to))Para$inclosure.to=inclosure.to
if(is.null(Para$inclosure.to))Para$inclosure.to=100
if(!is.null(inclosure.by)&is.null(Para$inclosure.by))Para$inclosure.by=inclosure.by
if(is.null(Para$inclosure.by))Para$inclosure.by=10
if(!is.null(bin.from)&is.null(Para$bin.from))Para$bin.from=bin.from
if(is.null(Para$bin.from))Para$bin.from=10000
if(!is.null(bin.to)&is.null(Para$bin.to))Para$bin.to=bin.to
if(is.null(Para$bin.to))Para$bin.to=10000
if(!is.null(bin.by)&is.null(Para$bin.by))Para$bin.by=bin.by
if(is.null(Para$bin.by))Para$bin.by=10000
if(!is.null(sangwich.top)&is.null(Para$sangwich.top))Para$sangwich.top=sangwich.top
if(is.null(Para$sangwich.top))Para$sangwich.top="MLM"
if(!is.null(sangwich.bottom)&is.null(Para$sangwich.bottom))Para$sangwich.bottom=sangwich.bottom
if(is.null(Para$sangwich.bottom))Para$sangwich.bottom="SUPER"
}
if(model=="FarmCPU")Para$kinship.algorithm="FarmCPU"
if(model=="MLMM")Para$kinship.algorithm="MLMM"
if(model=="Blink")Para$kinship.algorithm="Blink"
if(is.null(Para$memo)|m>1)Para$memo=model
print(Para$memo)
GAPIT_list=list(group.from=group.from ,group.to=group.to,group.by=group.by,DPP=DPP,kinship.cluster=kinship.cluster, kinship.group=kinship.group,kinship.algorithm=kinship.algorithm,
bin.from=bin.from,bin.to=bin.to,bin.by=bin.by,inclosure.from=inclosure.from,inclosure.to=inclosure.to,inclosure.by=inclosure.by,SNP.P3D=SNP.P3D,SNP.effect=SNP.effect,SNP.impute=SNP.impute,PCA.total=PCA.total, SNP.fraction = SNP.fraction, seed = seed, BINS = 20,SNP.test=SNP.test,
SNP.MAF=SNP.MAF,FDR.Rate = FDR.Rate, SNP.FDR=SNP.FDR,SNP.permutation=SNP.permutation,SNP.CV=NULL,SNP.robust="GLM",file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment,file.path=file.path,
file.G=file.G, file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,ngrid = 100, llim = -10, ulim = 10, esp = 1e-10,Inter.Plot=Inter.Plot,Inter.type=Inter.type,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,PCA.col=PCA.col,PCA.3d=PCA.3d,NJtree.group=NJtree.group,NJtree.type=NJtree.type,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,QC=QC,GTindex=GTindex,LD=LD,plot.bin=plot.bin,file.output=file.output,cutOff=cutOff, Model.selection = Model.selection,output.numerical = output.numerical,
output.hapmap = output.hapmap, Create.indicator = Create.indicator,QTN=QTN, QTN.round=1,QTN.limit=0, QTN.update=TRUE, QTN.method="Penalty", Major.allele.zero = Major.allele.zero,
method.GLM=method.GLM,method.sub=method.sub,method.sub.final="reward",method.bin="static",bin.size=bin.size,bin.selection=bin.selection,model=model,
h2=h2,NQTN=NQTN,QTNDist="normal",effectunit=effectunit,category=category,r=r,cveff=NULL,a2=0,adim=2,Multi_iter=Multi_iter,windowsize=5e9,
memo="",Prior=NULL,ncpus=1,maxLoop=maxLoop,threshold.output=threshold.output,WS=c(1e0,1e3,1e4,1e5,1e6,1e7),alpha=alpha,maxOut=100,QTN.position=QTN.position,CG=CG,
converge=converge,iteration.output=iteration.output,acceleration=0,iteration.method="accum",PCA.View.output=PCA.View.output,Geno.View.output=Geno.View.output,plot.style="Oceanic",SUPER_GD=NULL,SUPER_GS=SUPER_GS,Multiple_analysis=Multiple_analysis)
G_list_M=rownames(as.matrix(GAPIT_list))
P_list_M=rownames(as.matrix(Para))
Para=c(GAPIT_list[!G_list_M%in%P_list_M],Para)
#print(Para$kinship.algorithm)
if(SUPER_GS==TRUE)Para$SNP.test=FALSE
IC=NULL
#GAPIT.Version=GAPIT.0000()
print("--------------------Processing traits----------------------------------")
if(!is.null(Y)){
print("Phenotype provided!")
if(ncol(Y)<2) stop ("Phenotype should have taxa name and one trait at least. Please correct phenotype file!")
if(m==1)
{
DP=GAPIT.DP(G=G,GD=GD,GM=GM,KI=KI,Z=Z,CV=CV,CV.Inheritance=Para$CV.Inheritance,GP=GP,GK=GK,
group.from=Para$group.from ,group.to= Para$group.to,group.by=Para$group.by,DPP= Para$DPP,
kinship.cluster=Para$kinship.cluster, kinship.group=Para$kinship.group,kinship.algorithm=Para$ kinship.algorithm, NJtree.group=Para$NJtree.group,NJtree.type=Para$NJtree.type,plot.bin=Para$plot.bin,PCA.col=Para$PCA.col,PCA.3d=Para$PCA.3d,
sangwich.top=Para$sangwich.top,sangwich.bottom=Para$sangwich.bottom,LD=Para$LD,bin.from= Para$bin.from,bin.to= Para$bin.to,bin.by= Para$bin.by,inclosure.from= Para$inclosure.from,inclosure.to= Para$inclosure.to,inclosure.by= Para$inclosure.by,
SNP.P3D= Para$SNP.P3D,SNP.effect= Para$SNP.effect,SNP.impute= Para$SNP.impute,PCA.total= Para$PCA.total, SNP.fraction = Para$SNP.fraction, seed = Para$seed,
BINS = Para$BINS,SNP.test=Para$SNP.test, SNP.MAF= Para$SNP.MAF,FDR.Rate = Para$FDR.Rate, SNP.FDR= Para$SNP.FDR,SNP.permutation= Para$SNP.permutation,
SNP.CV= Para$SNP.CV,SNP.robust= Para$SNP.robust, Inter.Plot=Para$Inter.Plot, Inter.type=Para$Inter.type,
file.from= Para$file.from, file.to=Para$file.to, file.total= Para$file.total, file.fragment = Para$file.fragment,file.path= Para$file.path,
file.G= Para$file.G, file.Ext.G= Para$file.Ext.G,file.GD= Para$file.GD, file.GM= Para$file.GM, file.Ext.GD= Para$file.Ext.GD,file.Ext.GM= Para$file.Ext.GM,
ngrid = Para$ngrid, llim = Para$llim, ulim = Para$ulim, esp = Para$esp,Multi_iter=Para$Multi_iter,windowsize=Para$windowsize,
LD.chromosome= Para$LD.chromosome,LD.location= Para$LD.location,LD.range= Para$LD.range,
QC= Para$QC,GTindex= Para$GTindex,cutOff=Para$cutOff, Model.selection = Para$Model.selection,output.numerical = Para$output.numerical,
Create.indicator = Para$Create.indicator,QTN= Para$QTN, QTN.round= Para$QTN.round,QTN.limit= Para$QTN.limit, QTN.update= Para$QTN.update, QTN.method= Para$QTN.method, Major.allele.zero = Para$Major.allele.zero,
method.GLM=Para$ method.GLM,method.sub= Para$method.sub,method.sub.final= Para$method.sub.final,
method.bin= Para$method.bin,bin.size= Para$bin.size,bin.selection= Para$bin.selection,
memo= Para$memo,Prior= Para$Prior,ncpus=Para$ncpus,maxLoop= Para$maxLoop,threshold.output= Para$threshold.output,
WS= Para$WS,alpha= Para$alpha,maxOut= Para$maxOut,QTN.position= Para$QTN.position, converge=Para$converge,iteration.output= Para$iteration.output,acceleration=Para$acceleration,
iteration.method= Para$iteration.method,PCA.View.output=Para$PCA.View.output,
output.hapmap = Para$output.hapmap, file.output= Para$file.output,Geno.View.output=Para$Geno.View.output,plot.style=Para$plot.style,SUPER_GD= Para$SUPER_GD,SUPER_GS= Para$SUPER_GS,CG=Para$CG,model=model)
}else{
DP$kinship.algorithm=Para$ kinship.algorithm
DP$group.from=Para$group.from
DP$group.to=Para$group.to
DP$group.by=Para$group.by
DP$sangwich.top=Para$sangwich.top
DP$sangwich.bottom=Para$sangwich.bottom
DP$bin.from= Para$bin.from
DP$bin.to= Para$bin.to
DP$bin.by= Para$bin.by
DP$inclosure.from= Para$inclosure.from
DP$inclosure.to= Para$inclosure.toDP$inclosure.by= Para$inclosure.by
}
for (trait in 2: ncol(Y))
{
traitname=colnames(Y)[trait]
###Statistical distributions of phenotype
###Correlation between phenotype and principal components
print(paste("Processing trait: ",traitname,sep=""))
if(!is.null(Para$memo)) traitname=paste(Para$memo,".",traitname,sep="")
if(!is.null(Y) & Para$file.output)ViewPhenotype<-GAPIT.Phenotype.View(myY=Y[,c(1,trait)],traitname=traitname,memo=Para$memo)
Judge=GAPIT.Judge(Y=Y[,c(1,trait)],G=DP$G,GD=DP$GD,KI=DP$KI,GM=DP$GM,group.to=DP$group.to,group.from=DP$group.from,sangwich.top=DP$sangwich.top,sangwich.bottom=DP$sangwich.bottom,kinship.algorithm=DP$kinship.algorithm,PCA.total=DP$PCA.total,model=DP$model,SNP.test=DP$SNP.test)
DP$group.from=Judge$group.from
DP$group.to=Judge$group.to
DP$name.of.trait=traitname
DP$Y=Y[,c(1,trait)]
DP$model=model
print(Para$SNP.test)
IC=GAPIT.IC(DP=DP)
SS=GAPIT.SS(DP=DP,IC=IC)
if(Para$SNP.test==TRUE)ID=GAPIT.ID(DP=DP,IC=IC,SS=SS)
}#for loop trait
#print(SNP.test)
print("GAPIT accomplished successfully for multiple traits. Result are saved")
print("It is OK to see this: 'There were 50 or more warnings (use warnings() to see the first 50)'")
out <- list()
out$QTN<-QTN.position
out$GWAS<-SS$GWAS
out$Pred<-SS$Pred
out$QTN<-IC$QTN
out$Power<-SS$Power
out$FDR<-SS$FDR
out$Power.Alpha<-SS$Power.Alpha
out$alpha<-SS$alpha
out$mc=SS$mc
out$bc=SS$bc
out$mp=SS$mp
out$h2=SS$h2
out$PCA=IC$PCA
out$GD=DP$GD
out$GM=DP$GM
out$KI=IC$K
out$GM=DP$GM
if(Para$SNP.test==TRUE)names(out$GWAS$P.value)="mp"
if(kinship.algorithm=="FarmCPU")names(out$Pred)=c("Taxa",traitname,"Prediction")
#return (out)
}else{# is.null(Y)
#print(Para$SNP.MAF)
out <- list()
# if(is.null(Para$NQTN)&is.null(Para$h2))
# {
# Para$kinship.algorithm="SUPER"
# Para$PCA.total=0
# }
#print(Para$kinship.algorithm)
#print(Para$PCA.total)
myGenotype<-GAPIT.Genotype(G=G,GD=GD,GM=GM,KI=KI,kinship.algorithm=Para$kinship.algorithm,PCA.total=Para$PCA.total,SNP.fraction=Para$SNP.fraction,SNP.test=Para$SNP.test,
file.path=Para$file.path,file.from=Para$file.from, file.to=Para$file.to, file.total=Para$file.total, file.fragment = Para$file.fragment, file.G=Para$file.G,
file.Ext.G=Para$file.Ext.G,file.GD=Para$file.GD, file.GM=Para$file.GM, file.Ext.GD=Para$file.Ext.GD,file.Ext.GM=Para$file.Ext.GM,
SNP.MAF=Para$SNP.MAF,FDR.Rate = Para$FDR.Rate,SNP.FDR=Para$SNP.FDR,SNP.effect=Para$SNP.effect,SNP.impute=Para$SNP.impute,NJtree.group=Para$NJtree.group,NJtree.type=Para$NJtree.type,
LD.chromosome=Para$LD.chromosome,LD.location=Para$LD.location,LD.range=Para$LD.range,GP=Para$GP,GK=Para$GK,bin.size=NULL,inclosure.size=NULL,
sangwich.top=NULL,sangwich.bottom=Para$sangwich.bottom,GTindex=NULL,file.output=Para$file.output, Create.indicator = Para$Create.indicator, Major.allele.zero = Para$Major.allele.zero,Geno.View.output=Para$Geno.View.output,PCA.col=Para$PCA.col,PCA.3d=Para$PCA.3d)
GD=myGenotype$GD
GI=myGenotype$GI
GT=myGenotype$GT
#G=myGenotype$G
chor_taxa=myGenotype$chor_taxa
rownames(GD)=GT
colnames(GD)=GI[,1]
taxa=GT
#print(GD[1:5,1:5])
if(Para$output.numerical)
{
write.table(cbind(taxa,GD), "GAPIT.Genotype.Numerical.txt", quote = FALSE, sep = "\t", row.names = F,col.names = T)
write.table(GI, "GAPIT.Genotype.map.txt", quote = FALSE, sep = "\t", row.names = F,col.names = T)
}
if(Para$output.hapmap) write.table(myGenotype$G, "GAPIT.Genotype.hmp.txt", quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
#GD=cbind(as.data.frame(GT),GD)
if(!is.null(seed))set.seed(seed)
#print(Para$NQTN)
if(!is.null(Para$NQTN)&!is.null(Para$h2))
{
myG_simulation<-GAPIT.Phenotype.Simulation(GD=cbind(as.data.frame(myGenotype$GT),myGenotype$GD),GM=myGenotype$GI,h2=Para$h2,NQTN=Para$NQTN,QTNDist=Para$QTNDist,effectunit=Para$effectunit,category=Para$category,r=Para$r,cveff=Para$cveff,a2=Para$a2,adim=Para$adim)
out=c(out,myG_simulation)
}
out$GD=data.frame(cbind(as.data.frame(GT),as.data.frame(GD)))
out$GM=GI
out$G=myGenotype$G
out$kinship=myGenotype$KI
out$PCA=myGenotype$PC
}# is.null(Y)
}#end of model loop
#print(tail(IC$GM))
if(!is.null(Y)&SNP.test)if(Multiple_analysis&Para$file.output&length(model_store)*(ncol(Y)-1)>1&length(model_store)*(ncol(Y)-1)<9)
{
#print(DP$QTN.position)
GMM=GAPIT.Multiple.Manhattan(model_store=model_store,Y=Y,GM=IC$GM,seqQTN=DP$QTN.position)
#print(str(GMM$multip_mapP))
GAPIT.Circle.Manhatton.Plot(band=1,r=3,GMM$multip_mapP,plot.type=c("c","q"),signal.line=1,xz=GMM$xz)
}# end of mutiple manhantton plot
# if(!is.null(Y)&!SNP.test&Multiple_analysis&Para$file.output&length(model_store)*(ncol(Y)-1)>1)
# {
# GAPIT.Interactive.GS(model_store=model_store,Y=Y)
# }
return (out)
} #end of GAPIT function
`GAPIT.ROC` <-
function(t=NULL,se=NULL,Vp=1,trait="",plot.style="rainbow"){
#Object: To make table and plot for ROC (power vs FDR)
#Input: t and se are the vectors of t value and their standard error
#Input: Vp is phenotypic variance and trait is name of the phenotype
#Output: A table and plot
#Requirment: error df is same for all SMP or large
#Authors: Zhiwu Zhang
# Last update: Feb 11, 2013
##############################################################################################
#print("GAPIT.ROC start")
#print("Length of t se and Vp")
#print(length(t))
#print(length(se))
#print((Vp))
if(length(t)==length(t[is.na(t)]) ){
#print("NA t, No ROC plot")
return(NULL)
}
#test
#n=1000
#trait="test"
#t=rnorm(n)
#se=sqrt(abs(rnorm(n)) )
#Vp=10
#Remove NAs
index=is.na(t)
t=t[!index]
se=se[!index]
#print(head(cbind(t,se)))
#Configration
FDR=c(0,.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)
coefficient=c(0,0.01,.02,.05,.1,.2,.3)
#Power holder
nf=length(FDR)
nc=length(coefficient)
power=matrix(NA,nf,nc)
#Handler of matrix format
if(!is.null(dim(t))) t=t[,1]
if(!is.null(dim(se))) se=se[,1]
n=length(t)
#Discard negative
t=abs(t)
#print("@@@@@@@@@@@@@@")
#sort t and se
position=order(t,decreasing = TRUE)
t=t[position]
se=se[position]
EFFECT=coefficient*sqrt(Vp)
newbit=matrix(1/se,n,1)%*%EFFECT #n by nc matrix
tnew=newbit+t #n by nc matrix
for (i in 1:nf){
fdr=FDR[i]
cutpoint=floor(n*fdr)
cutoff=t[cutpoint]
for (j in 1:nc){
effect= EFFECT[j]
singnificant=tnew[,j]>cutoff
count=length(t[singnificant])
power[i,j]=count/n
} #end of for on fdr
} #end of for on effect
#output
rownames(power)=FDR
tkk<-c(.3,.2,.1,.05,.02,0.01,0)
tc1<-c(0,0.25,0.5,0.75,1.0)
#colnames(power)=paste("QTN=",coefficient,sep="")
colnames(power)=paste("QTN=",tkk,sep="")
if(plot.style=="FarmCPU"){
write.table(power,file=paste("FarmCPU.",trait,".ROC.csv",sep=""),quote = TRUE, sep = ",", row.names = TRUE,col.names = NA)
}
if(plot.style=="rainbow"){
write.table(power,file=paste("GAPIT.",trait,".ROC.csv",sep=""),quote = TRUE, sep = ",", row.names = TRUE,col.names = NA)
}
FDR_log<-FDR/10
#palette(c("black","red","blue","brown", "orange","cyan", "green",rainbow(nc)))
if(plot.style=="FarmCPU"){
pdf(paste("FarmCPU.", trait,".ROC.pdf" ,sep = ""), width = 5,height=5)
par(mar = c(5,6,5,3))
}
if(plot.style=="rainbow"){
pdf(paste("GAPIT.", trait,".ROC.pdf" ,sep = ""), width = 7,height=7)
par(mar = c(5,5,5,3))
}
palette(c("black","red","blue","brown", "orange","cyan", "green",rainbow(nc)))
plot(FDR_log,power[,1],log="x",type="o",yaxt="n",lwd=3,col=1,xlab="Type I error",ylab="Power",main = trait,cex.axis=1.3, cex.lab=1.3)
axis(side=2,at=tc1,labels=tc1,cex.lab=1.3,cex.axis=1.3)
for(i in 2:nc){
lines(power[,i]~FDR_log, lwd=3,type="o",pch=i,col=i)
}
#legend("bottomright", colnames(power), pch = c(1:nc), lty = c(1,2),col=c(1:nc))
legend("bottomright", colnames(power), pch = c(nc:1), lty = c(1,2),col=c(nc:1),lwd=2,bty="n")
palette("default") # reset back to the default
#print("@@@@@@@@@@@@@@")
#print(power)
dev.off()
print("ROC completed!")
} #GAPIT.ROC ends here
#=============================================================================================
`GAPIT.RandomModel` <-
function(GWAS,Y,CV=NULL,X,cutOff=0.01,GT=NULL,n_ran=30){
#Object: To calculate the genetics variance ratio of Candidate Genes
#Output: The genetics variance raito between CG and total
#Authors: Jiabo Wang and Zhiwu Zhang
# Last update: Nov 6, 2019
##############################################################################################
if(!require(lme4)) install.packages("lme4")
library("lme4")
#GWAS=myGAPIT_GLM$GWAS
#CV=myGAPIT_GLM$PCA
#cut.set=0.01
print("GAPIT.RandomModel beginning...")
if(is.null(GT))GT=as.character(Y[,1])
name.of.trait=colnames(Y)[2]
cutoff=cutOff/nrow(GWAS)
P.value=as.numeric(GWAS[,4])
P.value[is.na(P.value)]=1
index=P.value<cutoff
#index[c(1:2)]=TRUE
geneGD=X[,index]
geneGWAS=GWAS[index,]
# print(dim(Y))
# print(dim(CV))
# print(dim(geneGD))
if(length(unique(index))==1)
{
print("There is no significant marker for VE !!")
return(list(GVs=NULL))
}
index_T=as.matrix(table(index))
in_True=index_T[rownames(index_T)=="TRUE"]
if(in_True!=1)
{
colnames(geneGD)=paste("gene_",1:in_True,sep="")
}
colnames(Y)=c("taxa","trait")
if(is.null(CV))
{
#CV=cbind(GT,1)
taxa_Y=as.character(Y[,1])
geneGD=geneGD[GT%in%taxa_Y,]
# if(!is.null(PC))PC=PC[taxa_GD%in%taxa_Y,]
Y=Y[taxa_Y%in%GT,]
tree2=cbind(Y,geneGD)
# CV[,2]=1
}else{
if(ncol(CV)==1)
{
taxa_Y=as.character(Y[,1])
geneGD=geneGD[GT%in%taxa_Y,]
# if(!is.null(PC))PC=PC[taxa_GD%in%taxa_Y,]
Y=Y[taxa_Y%in%GT,]
tree2=cbind(Y,geneGD)
}else{
colnames(CV)=c("Taxa",paste("CV",1:(ncol(CV)-1),sep=""))
tree2=cbind(Y,CV[,-1],geneGD)
}
}
if(in_True==1)colnames(tree2)[ncol(tree2)]=paste("gene_",1,sep="")
# print(head(tree2))
# print(dim(CV))
# print(dim(geneGD))
n_cv=ncol(CV)-1
# print(n_cv)
n_gd=in_True
n_id=nrow(Y)
print(n_gd)
print(n_cv)
print(n_id)
if((n_gd+n_cv)>n_ran)
{
print("The candidate markers are more than threshold value !")
return(list(GVs=NULL))
}
if(!is.null(CV))
{
#ff <- paste("trait~1+PC1+PC2+PC3+(1|gene_1)+(1|gene_2)+(1|gene_3)+(1|gene_4)+(1|gene_5)+(1|gene_6)"
#dflme <- lmer(ff, data=tree2)
if(ncol(CV)==1)
{
command0=paste("trait~1",sep="")
command1=command0
command2=command1
for(j in 1:n_gd)
{
command2=paste(command2,"+(1|gene_",j,")",sep="")
}
}else{
command0=paste("trait~1",sep="")
command1=command0
for(i in 1:n_cv)
{
command1=paste(command1,"+CV",i,sep="")
}
command2=command1
for(j in 1:n_gd)
{
command2=paste(command2,"+(1|gene_",j,")",sep="")
}
}
}else{
command0=paste("trait~1",sep="")
command1=command0
command2=command1
for(j in 1:n_gd)
{
command2=paste(command2,"+(1|gene_",j,")",sep="")
}
}
#command3=paste(command2,"+(1|gene_",j,")",sep="")
dflme <- lmer(command2, data=tree2,control=lmerControl(check.nobs.vs.nlev = "ignore",
check.nobs.vs.rankZ = "ignore",
check.nobs.vs.nRE="ignore"))
carcor_matrix=as.data.frame(summary(dflme)$varcor)
var_gene=as.numeric(carcor_matrix[1:(nrow(carcor_matrix)-1),4])
var_res=carcor_matrix[nrow(carcor_matrix),4]
print(paste("Candidate Genes could explain genetics variance :",sep=""))
print(var_gene/sum(var_gene+var_res))
v_rat=var_gene/sum(var_gene+var_res)
gene_list=cbind(geneGWAS,v_rat)
colnames(gene_list)[ncol(gene_list)]="Variance_Explained"
write.csv(gene_list,paste("GAPIT.", name.of.trait,".Phenotype_Variance_Explained_by_Association_Markers.csv",sep=""),quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#gene_list=read.csv("GAPIT.Weight.GrowthIntercept.Phenotype_Variance_Explained_by_Association_Markers.csv",head=T)
if(!is.na(sum(gene_list[1,c(4:8)])))
{
pdf(paste("GAPIT.", name.of.trait,".Effect_VP.pdf" ,sep = ""), width = 7,height=5.75)
par(mar=c(4,5,4,4),cex=0.8)
gene_list=gene_list[order(gene_list$effect),]
plot(gene_list$effect,gene_list$Variance_Explained,
xlab="Estimated Effect",
ylab="Variance Explained of Phenotype"
)
dev.off()
pdf(paste("GAPIT.", name.of.trait,".MAF_VP.pdf" ,sep = ""), width = 7,height=5.75)
par(mar=c(4,5,4,4),cex=0.8)
gene_list=gene_list[order(gene_list$maf),]
plot(gene_list$maf,gene_list$Variance_Explained,xlab="MAF",ylab="Variance Explained of Phenotype")
dev.off()
if(n_gd>=10)
{
pdf(paste("GAPIT.", name.of.trait,".MAF_Effect_VP.pdf" ,sep = ""), width = 9,height=5.75)
n=10
layout(matrix(c(1,1,2,1,1,1,1,1,1),3,3,byrow=TRUE), c(2,1), c(1,1), TRUE)
do_color=colorRampPalette(c("green", "red"))(n)
par(mar=c(4,5,2,8),cex=0.8)
y=gene_list$maf
x=gene_list$effect
x.lim=max(x)+max(x)/10
y.lim=max(y)+max(y)/10
z=gene_list$Variance_Explained
quantile_cut=quantile(z)
r2_color=rep("black",n_gd)
for(i in 1:(n/2))
{
r2_color[z<=quantile_cut[i+1]&z>=quantile_cut[i]]=do_color[2*i]
}
plot(y~x,type="p", ylim=c(0,y.lim), xlim = c(min(x), max(x)),col = r2_color, xlab = "",ylab = "", cex.lab=1.2,pch=21,bg=r2_color)
mtext("Estimated Effect",side=1,line=2.5)
mtext("MAF",side=2,line=2.5)
par(mar=c(2,13,5,4),cex=0.5)
barplot(matrix(rep(0.4,times=n),n,1),beside=T,col=do_color,border=do_color,axes=FALSE,horiz =T)
#legend(x=10,y=2,legend=expression(R^"2"),,lty=0,cex=1.3,bty="n",bg=par("bg"))
step=length(seq(0,round(max(z),3),by=0.01))
small_bar=round(seq(0,round(max(z),3),by=(max(z)-min(z))/10),2)
#main()
mtext("Variance Explained",side=2,line=0.4,col="black",cex=0.5)
axis(4,c(1,6,11),c(min(small_bar),median(small_bar),max(small_bar)),las=2,cex.axis = 0.9,tick=F,line=0)
dev.off()
}
}
return(list(GVs=var_gene/sum(var_gene+var_res)))
}#end of GAPIT.RandomModel function
#=============================================================================================
`GAPIT.RemoveDuplicate` <-
function(Y){
#Object: NA
#Output: NA
#Authors: Zhiwu Zhang
# Last update: Augus 30, 2011
##############################################################################################
return (Y[match(unique(Y[,1]), Y[,1], nomatch = 0), ] )
}
#=============================================================================================
`GAPIT.Report` <-
function(name.of.trait=NULL,GWAS=NULL,pred=pred,ypred=NULL,tvalue=NULL,stderr=NULL,Vp=1,
DPP=100000,cutOff=.01,threshold.output=.01,MAF=NULL,seqQTN=NULL,MAF.calculate=FALSE,plot.style="rainbow"){
#Object: Out put plots and tables
#Input: GWAS,name.of.trait, DPP
#Requirement: None
#Output: Graphs and tables
#Output: return ycor if ypred is not null
#Authors: Zhiwu Zhang
# Date start: April 2, 2013
# Last update: April 2, 2013
##############################################################################################
#print("GAPIT.Report Started")
#print(seqQTN)
#Manhattan Plots
#print("Manhattan plot (Genomewise)..." )
if(plot.style=="FarmCPU"){
GAPIT.Manhattan(GI.MP = GWAS[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff,seqQTN=seqQTN,plot.style=plot.style)
}
if(plot.style=="rainbow"){
GAPIT.Manhattan(GI.MP = GWAS[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff,seqQTN=seqQTN,plot.style=plot.style)
#}
#print("Manhattan plot (Chromosomewise)..." )
GAPIT.Manhattan(GI.MP = GWAS[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Chromosomewise",cutOff=cutOff,plot.style=plot.style)
}
#QQ plots
#print("QQ plotting..." )
#if(plot.style=="rainbow"){
# GAPIT.QQ(P.values = GWAS[,4], name.of.trait = name.of.trait,DPP=DPP)
#}
#if(plot.style=="nature"){
GAPIT.QQ(P.values = GWAS[,4], name.of.trait = name.of.trait,DPP=DPP,plot.style=plot.style)
#}
#Association Table
#print("Create association table..." )
index=1:nrow(GWAS)
if(threshold.output<1)index=which(GWAS[,4]<threshold.output)
if(plot.style=="FarmCPU"){
write.table(GWAS[index,], paste("FarmCPU.", name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}
if(plot.style=="rainbow"){
write.table(GWAS[index,], paste("GAPIT.", name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}
#Prediction
#print("Create prediction table..." )
#if(!is.null(pred)) write.table(pred, paste("GAPIT.", name.of.trait, ".Pred.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#print("Create prediction table for unknown phenotype...")
#if(!is.null(ypred)) write.table(ypred, paste("GAPIT.", name.of.trait, ".unknownY.Pred.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
if(!is.null(pred) || !is.null(ypred)){
myPred=FarmCPU.Pred(pred=pred,ypred=ypred,name.of.trait=name.of.trait)
}
#ROC
#print("Creating ROC table and plot" )
myROC=GAPIT.ROC(t=tvalue,se=stderr,Vp=Vp,trait=name.of.trait,plot.style=plot.style)
#MAF
#print("Creating MAF table and plot" )
if(MAF.calculate){
myMAF=GAPIT.MAF(MAF=MAF,P=GWAS[,4],E=NULL,trait=name.of.trait,threshold.output=threshold.output,plot.style=plot.style)}
#print("Report accomplished" )
}#The function GAPIT.Report ends here
#=============================================================================================
`GAPIT.SS` <-
function(DP=NULL,IC=NULL){
#Object: To Sufficient Statistics (SS) for GWAS and GS
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("GAPIT.SS in process...")
#Define the funcitno here
Timmer=GAPIT.Timmer(Infor="GAPIT.SS")
Memory=GAPIT.Memory(Infor="GAPIT.SS")
if(DP$SNP.test)
{
ic_GD=IC$GD
ic_GM=IC$GM
ic_Y=IC$Y
ic_KI=IC$K
ic_PCA=IC$PCA
Z=DP$Z
taxa_Y=as.character(ic_Y[,1])
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GAPIT.QC")
Memory=GAPIT.Memory(Memory=Memory,Infor="GAPIT.QC")
if(DP$kinship.algorithm!="None" & DP$kinship.algorithm!="SUPER" & is.null(Z))
{
Z=as.data.frame(diag(1,nrow(ic_Y)))
Z=rbind(taxa_Y,Z)
taxa=c('Taxa',as.character(taxa_Y))
Z=cbind(taxa,Z)
}
# print(head(ic_PCA))
# print(dim(DP$CV))
# print(head(DP$PC))
if(max(ic_PCA[,2])==min(ic_PCA[,2]))ic_PCA=NULL
#print(head(ic_PCA))
#print("@@@@@")
if (DP$SNP.test&DP$kinship.algorithm%in%c("FarmCPU","Blink","MLMM"))
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GAPIT.FarmCPU")
Memory=GAPIT.Memory(Memory=Memory,Infor="GAPIT.FarmCPU")
myBus=GAPIT.Bus(Y=ic_Y,CV=ic_PCA,Z=NULL,GK=NULL,KI=ic_KI,GD=ic_GD,GM=ic_GM,GT=IC$GT,
method=DP$kinship.algorithm,GTindex=DP$GTindex,LD=DP$LD,
bin.size=DP$bin.size,bin.selection=DP$bin.selection,alpha=DP$alpha,WS=DP$WS,
cutOff=DP$cutOff,p.threshold=DP$p.threshold,QTN.threshold=DP$QTN.threshold,
maf.threshold=DP$maf.threshold,method.GLM=DP$method.GLM,method.sub=DP$method.sub,
method.sub.final=DP$method.sub.final,method.bin=DP$method.bin,
DPP=DP$DPP,file.output=DP$file.output,Multi_iter=DP$Multi_iter,windowsize=DP$windowsize )
GWAS=myBus$GWAS
Pred=myBus$GPS
va=myBus$vg
ve=myBus$ve
h2=va/(va+ve)
mc=NULL
#mc=(exp(1)^(1/GWAS$P.value))/10000
bc=NULL
mp=NULL
#myP=1/(exp(10000*fm$tau2)
#print(str(GWAS))
TV=NULL
Compression=NULL
GVs=myBus$GVs
}
#print(ic_GD[1:10,1:10])
if(!DP$kinship.algorithm%in%c("FarmCPU","MLMM","Blink"))
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GAPIT.Main")
Memory=GAPIT.Memory(Memory=Memory,Infor="GAPIT.Main")
GT=as.matrix(ic_GD[,1])
#print("!!!!!!!")
#print(DP$sangwich.top)
if(DP$PCA.total==0) ic_PCA=NULL
#print(dim(ic_PCA))
gapitMain <- GAPIT.Main(Y=ic_Y,GD=DP$GD[,-1],GM=DP$GM,KI=ic_KI,Z=Z,CV=DP$CV,CV.Inheritance=DP$CV.Inheritance,GP=DP$GP,GK=DP$GK,SNP.P3D=DP$SNP.P3D,kinship.algorithm=DP$kinship.algorithm,
bin.from=DP$bin.from,bin.to=DP$bin.to,bin.by=DP$bin.by,inclosure.from=DP$inclosure.from,inclosure.to=DP$inclosure.to,inclosure.by=DP$inclosure.by,
group.from=DP$group.from,group.to=DP$group.to,group.by=DP$group.by,kinship.cluster=DP$kinship.cluster,kinship.group=DP$kinship.group,name.of.trait=DP$name.of.trait,
file.path=DP$file.path,file.from=DP$file.from, file.to=DP$file.to, file.total=DP$file.total, file.fragment = DP$file.fragment, file.G=DP$file.G,file.Ext.G=DP$file.Ext.G,file.GD=DP$file.GD, file.GM=DP$file.GM, file.Ext.GD=DP$file.Ext.GD,file.Ext.GM=DP$file.Ext.GM,
SNP.MAF= DP$SNP.MAF,FDR.Rate = DP$FDR.Rate,SNP.FDR=DP$SNP.FDR,SNP.effect=DP$SNP.effect,SNP.impute=DP$SNP.impute,PCA.total=DP$PCA.total,GAPIT.Version=GAPIT.Version,
GT=GT, SNP.fraction = DP$SNP.fraction, seed =DP$ seed, BINS = DP$BINS,SNP.test=DP$SNP.test,DPP=DP$DPP, SNP.permutation=DP$SNP.permutation,
LD.chromosome=DP$LD.chromosome,LD.location=LD.location,LD.range=LD.range,SNP.CV=SNP.CV,SNP.robust=DP$SNP.robust,model=DP$model,
genoFormat="EMMA",hasGenotype=TRUE,byFile=FALSE,fullGD=TRUE,PC=DP$PC,GI=ic_GM,Timmer = DP$Timmer, Memory = DP$Memory,
sangwich.top=DP$sangwich.top,sangwich.bottom=DP$sangwich.bottom,QC=DP$QC,GTindex=DP$GTindex,LD=DP$LD,file.output=FALSE,cutOff=DP$cutOff, GAPIT3.output=DP$file.output,
Model.selection = DP$Model.selection, Create.indicator = DP$Create.indicator,
QTN=DP$QTN, QTN.round=DP$QTN.round,QTN.limit=DP$QTN.limit, QTN.update=QTN.update, QTN.method=DP$QTN.method, Major.allele.zero=DP$Major.allele.zero,NJtree.group=DP$NJtree.group,NJtree.type=DP$NJtree.type,plot.bin=DP$plot.bin,
QTN.position=DP$QTN.position,plot.style=DP$plot.style,SUPER_GS=DP$SUPER_GS)
#print(str(gapitMain))
GWAS=gapitMain$GWAS
GR=GAPIT.RandomModel(Y=ic_Y,X=DP$GD[,-1],GWAS=GWAS,CV=gapitMain$PC,cutOff=DP$cutOff,GT=IC$GT)
Pred=gapitMain$Pred
#print(head(Pred))
va=NA#gapitMain$vg
ve=NA#gapitMain$ve
h2=gapitMain$h2
mc=gapitMain$effect.snp
bc=gapitMain$effect.cv
mp=gapitMain$P
TV=gapitMain$TV
Compression=gapitMain$Compression
GVs=GR$GVs
}
myPower=NULL
#print(head(GWAS))
#print(DP$QTN.position)
if(!is.null(GWAS))myPower=GAPIT.Power(WS=DP$WS, alpha=DP$alpha, maxOut=DP$maxOut,seqQTN=DP$QTN.position,GM=DP$GM,GWAS=GWAS)
#print(str(myPower))
#print("GAPIT.III accomplished successfully for multiple traits. Results are saved")
return (list(GWAS=GWAS,Pred=Pred,FDR=myPower$FDR,Power=myPower$Power,
Power.Alpha=myPower$Power.Alpha,alpha=myPower$alpha,h2=h2,va=va,ve=ve,
mc=mc,bc=bc,mp=mp,TV=TV,Compression=Compression,
Timmer=Timmer,Memory=Memory,GVs=GVs))
}else{
#
# print("!!!!!!!!!")
# print(dim(DP$Y))
# print(dim(DP$GD))
# print(dim(DP$CV))
# print(dim(DP$PC))
gapitMain <- GAPIT.Main(Y=DP$Y,GD=DP$GD[,-1],GM=DP$GM,KI=DP$KI,Z=DP$Z,CV=DP$CV,CV.Inheritance=DP$CV.Inheritance,GP=DP$GP,GK=DP$GK,SNP.P3D=DP$SNP.P3D,kinship.algorithm=DP$kinship.algorithm,
bin.from=DP$bin.from,bin.to=DP$bin.to,bin.by=DP$bin.by,inclosure.from=DP$inclosure.from,inclosure.to=DP$inclosure.to,inclosure.by=DP$inclosure.by,
group.from=DP$group.from,group.to=DP$group.to,group.by=DP$group.by,kinship.cluster=DP$kinship.cluster,kinship.group=DP$kinship.group,name.of.trait=DP$name.of.trait,
file.path=DP$file.path,file.from=DP$file.from, file.to=DP$file.to, file.total=DP$file.total, file.fragment = DP$file.fragment, file.G=DP$file.G,file.Ext.G=DP$file.Ext.G,file.GD=DP$file.GD, file.GM=DP$file.GM, file.Ext.GD=DP$file.Ext.GD,file.Ext.GM=DP$file.Ext.GM,
SNP.MAF= DP$SNP.MAF,FDR.Rate = DP$FDR.Rate,SNP.FDR=DP$SNP.FDR,SNP.effect=DP$SNP.effect,SNP.impute=DP$SNP.impute,PCA.total=DP$PCA.total,GAPIT.Version=GAPIT.Version,
GT=DP$GT, SNP.fraction = DP$SNP.fraction, seed =DP$ seed, BINS = DP$BINS,SNP.test=DP$SNP.test,DPP=DP$DPP, SNP.permutation=DP$SNP.permutation,
LD.chromosome=DP$LD.chromosome,LD.location=LD.location,LD.range=LD.range,SNP.CV=SNP.CV,SNP.robust=DP$SNP.robust,model=DP$model,
genoFormat="EMMA",hasGenotype=TRUE,byFile=FALSE,fullGD=TRUE,PC=DP$PC,GI=DP$GI,Timmer = DP$Timmer, Memory = DP$Memory,GAPIT3.output=DP$file.output,
sangwich.top=DP$sangwich.top,sangwich.bottom=DP$sangwich.bottom,QC=DP$QC,GTindex=DP$GTindex,LD=DP$LD,file.output=FALSE,cutOff=DP$cutOff,
Model.selection = DP$Model.selection, Create.indicator = DP$Create.indicator,
QTN=DP$QTN, QTN.round=DP$QTN.round,QTN.limit=DP$QTN.limit, QTN.update=QTN.update, QTN.method=DP$QTN.method, Major.allele.zero=DP$Major.allele.zero,NJtree.group=DP$NJtree.group,NJtree.type=DP$NJtree.type,plot.bin=DP$plot.bin,
QTN.position=DP$QTN.position,plot.style=DP$plot.style,SUPER_GS=DP$SUPER_GS)
#print(str(gapitMain))
GWAS=gapitMain$GWAS
#print(head(GWAS))
Pred=gapitMain$Pred
#print(head(Pred))
va=NA#gapitMain$vg
ve=NA#gapitMain$ve
h2=gapitMain$h2
mc=gapitMain$effect.snp
bc=gapitMain$effect.cv
mp=gapitMain$P
Compression=gapitMain$Compression
return (list(GWAS=GWAS,Pred=Pred,FDR=NULL,Power=NULL,
Power.Alpha=NULL,alpha=NULL,h2=h2,va=va,ve=ve,Compression=Compression,
mc=mc,bc=bc,mp=mp,TV=gapitMain$TV,
Timmer=Timmer,Memory=Memory))
}#end of SNP.TEST
} #end of GAPIT.SS function
#=============================================================================================
`GAPIT.SUPER.FastMLM` <-
function(ys, xs, vg, delta, Z = NULL, X0 = NULL, snp.pool=NULL,LD=0.01,method="FaST") {
#Input: ys, xs, vg, delta, Z, X0, snp.pool
#Output: GWAS
#Authors: Qishan Wang, Feng Tian and Zhiwu Zhang
#Last update: April 16, 2012
################################################################################
#print("GAPIT.SUPER.FastMLM started")
#print("dimension of ys,xs,X0 and snp.pool")
#print(length(ys))
#print(dim(xs))
#print(dim(X0))
#print(dim(snp.pool))
#print((LD))
#Set data to the require format
ys=unlist(ys)
if(is.null(dim(ys)) || ncol(ys) == 1) ys <- matrix(ys, 1, length(ys))
if(is.null(dim(xs)) || ncol(xs) == 1) xs <- matrix(xs, 1, length(xs))
if(is.null(X0)) X0 <- matrix(1, nrow(snp.pool), 1)
#Exract data size
g <- nrow(ys)
n <- nrow(xs) ##### generaol nrow(xs)=nrow(U1) rivised by qishan 2012.4.16
m <- ncol(xs)
t <- nrow(xs)
q0 <- ncol(X0)
q1 <- q0 + 1
#Allocate space
dfs <- matrix(nrow = m, ncol = g)
stats <- matrix(nrow = m, ncol = g)
ps <- matrix(nrow = m, ncol = g)
betavalue <- matrix(nrow = m, ncol = g)
####################
if(method=="SUPER"){
LDsqr=sqrt(LD)
##################
#Iteration on trait (j) and SNP (i)
for(j in 1:g)
{
for (i in 1:m)
{
if((i >0)&(floor(i/500)==i/500)) print(paste("SNP: ",i," ",sep=""))
#No variation on the SNP
if(min(xs[,i])==max(xs[,i]))
{
dfs[i,j] <- n - q1
betavalue[i,j]=0
stats[i,j] <- 0
}
#The SNP has variation
if(min(xs[,i])!=max(xs[,i]))
{
#SUPER
snp.corr=cor(xs[,i],snp.pool)
index.k=which( abs(snp.corr)<=LDsqr )
#handler of snp correlated with all QTNs
if(length(index.k)<2){
index.k=1:length(snp.corr) #keep going to have them all
#print("warning: there is a snp correlated with all QTNs")
}
K.X= snp.pool[,index.k]
####################
K.X.svd= svd(K.X) ###start 2012.4.16 by qishan
d=K.X.svd$d
d=d[d>1e-8]
d=d^2
U1=K.X.svd$u
U1=U1[,1:length(d)] ### end 2012.4.16 by qishan
n<-nrow(U1)
I= diag(1,nrow(U1))
################ get iXX
X <- cbind(X0, xs[,i]) ####marker by column
U <- U1*matrix(sqrt(1/(d + delta)), nrow(U1), length(d), byrow = TRUE)
Xt <- crossprod(U, X)
XX1<- crossprod(Xt, Xt)
XX2<- crossprod((I-tcrossprod(U1,U1))%*%X,(I-tcrossprod(U1,U1))%*%X)/delta
#iXX<-solve(XX1+XX2)
iXX <- try(solve(XX1+XX2),silent=T)
if(inherits(iXX, "try-error")){
iXX <- ginv(XX1+XX2)
}
################# end get ixx
################ begin get beta
################
#######get beta compnents 1
#U1TX=t(U1)%*%X
U1TX=crossprod(U1,X)
beta1=0
for(ii in 1:length(d)){
one=matrix(U1TX[ii,], nrow=1)
dim(one)
#beta=t(one)%*%one/(d[ii]+delta)
beta=crossprod(one,one)/(d[ii]+delta)
beta1= beta1+beta
}
#######get beta components 2
#IUX=(I-U1%*%t(U1))%*%X
IUX=(I-tcrossprod(U1,U1))%*%X
beta2=0
for(ii in 1:nrow(U1)){
one=matrix(IUX[ii,], nrow=1)
dim(one)
beta=t(one)%*%one
beta2= beta2+beta
}
beta2<-beta2/delta
#######get b3
#U1TY=t(U1)%*%ys[j,]
U1TY=crossprod(U1,ys[j,])
beta3=0
for(ii in 1:length(d)){
one1=matrix(U1TX[ii,], nrow=1)
one2=matrix(U1TY[ii,], nrow=1)
beta=crossprod(one1,one2)/(d[ii]+delta)
beta3= beta3+beta
}
###########get beta4
#IUY=(I-U1%*%t(U1))%*%ys[j,]
IUY=(I-tcrossprod(U1,U1))%*%ys[j,]
beta4=0
for(ii in 1:nrow(U1)){
one1=matrix(IUX[ii,], nrow=1)
one2=matrix(IUY[ii,], nrow=1)
#beta=t(one1)%*%one2
beta=crossprod(one1,one2)
beta4= beta4+beta
}
beta4<-beta4/delta
#######get final beta
beta=ginv(beta1+beta2)%*%(beta3+beta4)
##############
################ end get beta
betavalue[i,j]=beta[q1,1]
stats[i,j] <- beta[q1,1]/sqrt(iXX[q1, q1] * vg)
dfs[i,j] <- n - q1
} #end of SNP variation stutus detection
} #loop for markers
#print("Calculating p-values...")
ps[,j] <- 2 * pt(abs(stats[,j]), dfs[,j], lower.tail = FALSE)
} #end of loop on traits
return(list(beta=betavalue, ps = ps, stats = stats, dfs = dfs,effect=betavalue))
} #Enf of SUPERMLM
#######################
if(method=="FaST"){
K.X.svd= svd(snp.pool) ###start 2012.4.16 by qishan
d=K.X.svd$d
d=d[d>1e-8]
d=d^2
U1=K.X.svd$u
U1=U1[,1:length(d)] ### end 2012.4.16 by qishan
n<-nrow(U1)
I= diag(1,nrow(U1))
U <- U1*matrix(sqrt(1/(d + delta)), nrow(U1), length(d), byrow = TRUE)
##################
#Iteration on trait (j) and SNP (i)
for(j in 1:g)
{
for (i in 1:m)
{
if((i >0)&(floor(i/500)==i/500)) print(paste("SNP: ",i," ",sep=""))
#No variation on the SNP
if(min(xs[,i])==max(xs[,i]))
{
dfs[i,j] <- n - q1
betavalue[i,j]=0
stats[i,j] <- 0
}
#The SNP has variation
if(min(xs[,i])!=max(xs[,i]))
{
#SUPER
####################
K.X.svd= svd(snp.pool) ###start 2012.4.16 by qishan
d=K.X.svd$d
d=d[d>1e-8]
d=d^2
U1=K.X.svd$u
U1=U1[,1:length(d)] ### end 2012.4.16 by qishan
n<-nrow(U1)
I= diag(1,nrow(U1))
################ get iXX
X <- cbind(X0, xs[,i]) ####marker by column
U <- U1*matrix(sqrt(1/(d + delta)), nrow(U1), length(d), byrow = TRUE)
Xt <- crossprod(U, X)
XX1<- crossprod(Xt, Xt)
XX2<- crossprod((I-tcrossprod(U1,U1))%*%X,(I-tcrossprod(U1,U1))%*%X)/delta
iXX <- try(solve(XX1+XX2),silent=T)
if(inherits(iXX, "try-error")){
iXX <- ginv(XX1+XX2)
}
################# end get ixx
################ begin get beta
#######get beta compnents 1
#U1TX=t(U1)%*%X
U1TX=crossprod(U1,X)
beta1=0
for(ii in 1:length(d)){
one=matrix(U1TX[ii,], nrow=1)
dim(one)
beta=crossprod(one,one)/(d[ii]+delta)
beta1= beta1+beta
}
#######get beta components 2
IUX=(I-tcrossprod(U1,U1))%*%X
beta2=0
for(ii in 1:nrow(U1)){
one=matrix(IUX[ii,], nrow=1)
dim(one)
beta=crossprod(one,one)
beta2= beta2+beta
}
beta2<-beta2/delta
#######get b3
#U1TY=t(U1)%*%ys[j,]
U1TY=crossprod(U1,ys[j,])
beta3=0
for(ii in 1:length(d)){
one1=matrix(U1TX[ii,], nrow=1)
one2=matrix(U1TY[ii,], nrow=1)
#beta=t(one1)%*%one2/(d[ii]+delta)
beta=crossprod(one1,one2)/(d[ii]+delta)
beta3= beta3+beta
}
###########get beta4
#IUY=(I-U1%*%t(U1))%*%ys[j,]
IUY=(I-tcrossprod(U1,U1))%*%ys[j,]
beta4=0
for(ii in 1:nrow(U1)){
one1=matrix(IUX[ii,], nrow=1)
one2=matrix(IUY[ii,], nrow=1)
#beta=t(one1)%*%one2
beta=crossprod(one1,one2)
beta4= beta4+beta
}
beta4<-beta4/delta
#######get final beta
beta=ginv(beta1+beta2)%*%(beta3+beta4)
##############
################ end get beta
betavalue[i,j]=beta[q1,1]
stats[i,j] <- beta[q1,1]/sqrt(iXX[q1, q1] * vg)
dfs[i,j] <- n - q1
} #end of SNP variation stutus detection
} #loop for markers
#print("Calculating p-values...")
ps[,j] <- 2 * pt(abs(stats[,j]), dfs[,j], lower.tail = FALSE)
} #end of loop on traits
return(list(beta=betavalue, ps = ps, stats = stats, dfs = dfs,effect=betavalue))
} #Enf of FastMLM
}####end function
#=============================================================================================
`GAPIT.SUPER.GS`<-
function(Y=Y[,c(1,trait)],G=NULL,GD=NULL,GM=NULL,KI=NULL,Z=NULL,CV=NULL,GK=GK,kinship.algorithm=kinship.algorithm,
bin.from=bin.from,bin.to=bin.to,bin.by=bin.by,inclosure.from=inclosure.from,inclosure.to=inclosure.to,inclosure.by=inclosure.by,
group.from=group.from,group.to=group.to,group.by=group.by,kinship.cluster=kinship.cluster,kinship.group=kinship.group,name.of.trait=traitname,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF= SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,PCA.total=PCA.total,GAPIT.Version=GAPIT.Version,
GT=GT, SNP.fraction = SNP.fraction, seed = seed, BINS = BINS,SNP.test=SNP.test,DPP=DPP, SNP.permutation=SNP.permutation,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,SNP.CV=SNP.CV,SNP.robust=SNP.robust,model=model,
genoFormat=genoFormat,hasGenotype=hasGenotype,byFile=byFile,fullGD=fullGD,PC=PC,GI=GI,Timmer = Timmer, Memory = Memory,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,QC=QC,GTindex=GTindex,LD=LD,file.output=file.output,cutOff=cutOff
){
#Object: To perform GPS with SUPER and Compress method
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novber 6, 2015
######################################################
print("--------------------- Welcome to GAPIT SUPER GS----------------------------")
Timmer=GAPIT.Timmer(Infor="GAPIT.SUPER.GS")
Memory=GAPIT.Memory(Infor="GAPIT.SUPER.GS")
if(!require(EMMREML)) install.packages("EMMREML")
library(EMMREML)
shortcut=FALSE
LL.save=1e10
#In case of null Y and null GP, return genotype only
thisY=Y[,2]
thisY=thisY[!is.na(thisY)]
if(length(thisY) <3){
shortcut=TRUE
}else{
if(var(thisY) ==0) shortcut=TRUE
}
if(shortcut){
print(paste("Y is empty. No GWAS/GS performed for ",name.of.trait,sep=""))
return (list(compression=NULL,kinship.optimum=NULL, kinship=KI,PC=PC,GWAS=NULL, GPS=NULL,Pred=NULL, REMLs=NULL,Timmer=Timmer,Memory=Memory))
}
print("------------Examining data (QC)------------------------------------------")
if(is.null(Y)) stop ("GAPIT says: Phenotypes must exist.")
if(is.null(KI)&missing(GD) & kinship.algorithm!="SUPER") stop ("GAPIT says: Kinship is required. As genotype is not provided, kinship can not be created.")
if(is.null(GD) & is.null(GT)) {
GT=as.matrix(Y[,1])
GD=matrix(1,nrow(Y),1)
GI=as.data.frame(matrix(0,1,3) )
colnames(GI)=c("SNP","Chromosome","Position")
}
#merge CV with PC
#print(dim(CV))
#if(PCA.total>0&!is.null(CV))CV=GAPIT.CVMergePC(CV,PC)
#if(PCA.total>0&is.null(CV))CV=PC
#for GS merge CV with GD name
#print("!!!!!!")
#print(dim(CV))
# print(head(GT))
# print(head(GI))
# if (is.null(CV))
# {my_allCV=CV
# }else{
# taxa_GD=GT
# my_allCV=CV[order(CV[,1]),]
# my_allCV=my_allCV[my_allCV[,1]%in%taxa_GD,]
# #print(dim(my_allCV))
# }
my_allCV=CV
#print(dim(my_allCV))
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & is.null(Z)){
taxa=as.character(Y[,1])
Z=as.data.frame(diag(1,nrow(Y)))
Z=rbind(taxa,Z)
taxa=c('Taxa',as.character(taxa))
Z=cbind(taxa,Z)
}
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & !is.null(Z))
{
if(nrow(Z)-1<nrow(Y)) Z=GAPIT.ZmatrixFormation(Z=Z,Y=Y)
}
noCV=FALSE
if(is.null(CV)){
noCV=TRUE
CV=Y[,1:2]
CV[,2]=1
colnames(CV)=c("taxa","overall")
}
#Remove duplicat and integragation of data
print("QC is in process...")
CVI <- CV
if(QC)
{
#print(colnames(KI)[53:62])
qc <- GAPIT.QC(Y=Y,KI=KI, GT=GT,CV=CV,Z=Z,GK=GK)
GTindex=qc$GTindex
Y=qc$Y
KI=qc$KI
CV=qc$CV
Z=qc$Z
GK=qc$GK
my_taxa=as.character(KI[,1])
my_allKI=KI
#print(dim(CV))
}
print("The value of QC is")
print(QC)
rm(qc)
gc()
print("------------Examining data (QC) done-------------------------------------")
super_pass=FALSE
SUPER_myKI=NULL
SUPER_optimum_GD=NULL
if (!is.null(sangwich.top)) super_pass=TRUE
if(super_pass)
{
print("-------------------start SUPER BREAD-----------------------------------")
#Create GK if not provided
#print(memory.size())
if(is.null(GK)){
nY=floor(nrow(Y)*.9)
nG=ncol(GD)
if(nG>nY){snpsam=sample(1:nG,nY)}else{snpsam=1:nG}
GK=GD[GTindex,snpsam]
SNPVar=apply(as.matrix(GK),2,var)
#print(snpsam)
if (snpsam==1)stop ("GAPIT says: SUPER_GS must putin GD and GM.")
GK=GK[,SNPVar>0]
GK=cbind(as.data.frame(GT[GTindex]),as.data.frame(GK)) #add taxa
}
#print(head(CV))
#myGD=cbind(as.data.frame(GT),as.data.frame(GD))
file.output.temp=file.output
file.output=FALSE
# print(memory.size())
GP=GAPIT.Bread(Y=Y,CV=CV,Z=Z,KI=KI,GK=GK,GD=cbind(as.data.frame(GT),as.data.frame(GD)),GM=GI,method=sangwich.top,GTindex=GTindex,LD=LD,file.output=file.output)$GWAS
file.output=file.output.temp
# print(memory.size())
GK=NULL
if(inclosure.to>nrow(Y)) ##########removed by Jiabo Wang ,unlimited number of inclosures
{
inclosure.to=nrow(Y)-1
print("the number of choosed inclosure is more than number of individuals")
print("Set the number of choosed incolosure max equal to individuals")
}
if(inclosure.from>inclosure.to) ##########removed by Jiabo Wang ,unlimited number of inclosures
{
inclosure.from=inclosure.to
}
bin.level=seq(bin.from,bin.to,by=bin.by)
inclosure=seq(inclosure.from,inclosure.to,by=inclosure.by)
#print(inclosure)
e=1 #################################number of bins and inclosure
count=0
num_selection=length(bin.level)*length(inclosure)
SUPER_selection=matrix(,num_selection,6)
colnames(SUPER_selection)=c("bin","pseudo_QTNs","Max_pQTNs","REML","VA","VE")
#for (bin in bin.level){bin=bin.level[e]}
#for (inc in inclosure){inc=inclosure[e]}
for (bin in bin.level){
for (inc in inclosure){
count=count+1
mySpecify=GAPIT.Specify(GI=GI,GP=GP,bin.size=bin,inclosure.size=inc)
SNP.QTN=mySpecify$index
num_pseudo_QTN=length(mySpecify$CB)
num_bins=mySpecify$num_bins
#print(paste("bin---",bin,"---inc---",inc,sep=""))
GK=GD[GTindex,SNP.QTN]
SUPER_GD=GD[,SNP.QTN]
SNPVar=apply(as.matrix(GK),2,var)
GK=GK[,SNPVar>0]
SUPER_GD=SUPER_GD[,SNPVar>0]
GK=cbind(as.data.frame(GT[GTindex]),as.data.frame(GK)) #add taxa
SUPER_GD=cbind(as.data.frame(GT),as.data.frame(SUPER_GD)) #add taxa
myBurger=GAPIT.Burger(Y=Y,CV=CV,GK=GK) #modifed by Jiabo Wang
myREML=myBurger$REMLs
myVG=myBurger$vg
myVE=myBurger$ve
SUPER_selection[count,1]=bin
SUPER_selection[count,2]=num_pseudo_QTN
SUPER_selection[count,3]=num_bins
SUPER_selection[count,4]=myREML
SUPER_selection[count,5]=myVG
SUPER_selection[count,6]=myVE
#print(SUPER_selection[count,])
if(count==1){
GK.save=GK
LL.save=myREML
SUPER_optimum_GD=SUPER_GD ########### get SUPER GD
}else{
if(myREML<LL.save){
GK.save=GK
LL.save=myREML
SUPER_optimum_GD=SUPER_GD ########### get SUPER GD
}
}
if (num_bins==num_pseudo_QTN) break
}# bin end
}# inc end
SUPER_selection<-SUPER_selection[!is.na(SUPER_selection[,1]),]
print(SUPER_selection)
print("-----select optimum pseudo QTNs from all the bins-------")
if(is.null(dim(SUPER_selection)))
{optimum_SUPER=SUPER_selection
}else{
optimum_SUPER=SUPER_selection[which(as.numeric(SUPER_selection[,4])==min(as.numeric(SUPER_selection[,4]))),]
}
print(optimum_SUPER)
########################BUILD SUPER KINSHIP
##########################################################
colnames(SUPER_optimum_GD)=c("taxa",colnames(SUPER_optimum_GD)[-1])
SUPER_taxa=as.character(SUPER_optimum_GD[,1])
SUPER_X=SUPER_optimum_GD[,-1]
if(kinship.algorithm=="Loiselle")SUPER_myKI_test= GAPIT.kinship.loiselle(snps=t(as.matrix(.5*(SUPER_optimum_GD[,-1]))), method="additive", use="all")
# if(kinship.algorithm=="VanRaden")SUPER_myKI_test= GAPIT.kinship.VanRaden(snps=as.matrix(SUPER_optimum_GD[,-1]))
if(kinship.algorithm=="Zhang")SUPER_myKI_test= GAPIT.kinship.ZHANG(snps=as.matrix(SUPER_optimum_GD[,-1]))
if(!kinship.algorithm=="Loiselle"|!kinship.algorithm=="Zhang")SUPER_myKI_test= GAPIT.kinship.VanRaden(snps=as.matrix(SUPER_optimum_GD[,-1]))
SUPER_myKI_test=GAPIT.kinship.VanRaden(snps=as.matrix(SUPER_optimum_GD[,-1])) # build kinship
colnames(SUPER_myKI_test)=SUPER_taxa
SUPER_myKI=cbind(SUPER_taxa,as.data.frame(SUPER_myKI_test))
print("select optimum number of marker effect in GD")
print(dim(SUPER_optimum_GD))
#print(SUPER_optimum_GD[1:5,1:5])
######################################GOIN TO NEW CBLUP
Z=NULL
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & is.null(Z)){
taxa=as.character(SUPER_optimum_GD[,1])
Z=as.data.frame(diag(1,nrow(SUPER_optimum_GD)))
Z=rbind(taxa,Z)
taxa=c('Taxa',as.character(taxa))
Z=cbind(taxa,Z)
}
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & !is.null(Z))
{
if(nrow(Z)-1<nrow(Y)) Z=GAPIT.ZmatrixFormation(Z=Z,Y=Y)
}
print("QC is in process...")
GK=NULL
CVI <- CV
if(QC)
{
qc <- GAPIT.QC(Y=Y,KI=SUPER_myKI, GT=GT,CV=CV,Z=Z,GK=GK)
GTindex=qc$GTindex
Y=qc$Y
KI=qc$KI
CV=qc$CV
Z=qc$Z
GK=qc$GK
}
rm(qc)
gc()
}# super_pass end
nk=1000000000
if(!is.null(KI)) nk=min(nk,nrow(KI))
if(!is.null(GK)) nk=min(nk,nrow(GK))
if(!is.null(KI))
{
if(group.to>nk) {
#group.to=min(nrow(KI),length(GTindex)) #maximum of group is number of rows in KI
group.to=nk #maximum of group is number of rows in KI
warning("The upper bound of groups is too high. It was set to the size of kinship!")
}
if(group.from>nk){
group.from=nk
warning("The lower bound of groups is too high. It was set to the size of kinship!")
}
}
if(!is.null(CV)){
if(group.to<=ncol(CV)+1) {
#The minimum of group is number of columns in CV
group.from=ncol(CV)+2
group.to=ncol(CV)+2
warning("The upper bound of groups (group.to) is not sufficient. both boundries were set to their minimum and GLM is performed!")
}
}
GROUP=seq(group.to,group.from,by=-group.by)#The reverse order is to make sure to include full model
if(missing("kinship.cluster")) kinship.cluster=c("ward", "single", "complete", "average", "mcquitty", "median", "centroid")
if(missing("kinship.group")) kinship.group=c("Mean", "Max", "Min", "Median")
numSetting=length(GROUP)*length(kinship.cluster)*length(kinship.group)
ys=as.matrix(Y[2])
X0=as.matrix(CV[,-1])
if(min(X0[,1])!=max(X0[,1])) X0 <- cbind(1, X0) #do not add overall mean if X0 has it already at first column
hold_Z=Z
# library("EMMREML")
order_count=0
storage_reml=NULL
Compression=matrix(,numSetting,6)
colnames(Compression)=c("Type","Cluster","Group","REML","VA","VE")
for (group in GROUP)
{
for (ca in kinship.cluster)
{
for (kt in kinship.group)
{
#if(group=1) group=2
#if(!optOnly) {print("Compressing and Genome screening..." )}
order_count=order_count+1
if(order_count==1)print("-------Mixed model with Kinship-----------------------------")
if(group<ncol(X0)+1) group=2 # the emma function (emma.delta.REML.dLL.w.Z) does not allow K has dim less then CV. turn to GLM (group=1)
cp <- GAPIT.Compress(KI=KI,kinship.cluster=ca,kinship.group=kt,GN=group,Timmer=Timmer,Memory=Memory)
bk <- GAPIT.Block(Z=hold_Z,GA=cp$GA,KG=cp$KG)
zc <- GAPIT.ZmatrixCompress(Z=hold_Z,GAU =bk$GA)
zrow=nrow(zc$Z)
zcol=ncol(zc$Z)-1
K = as.matrix(bk$KW)
#if (nrow(as.matrix(bk$KW))==1)
Z=matrix(as.numeric(as.matrix(zc$Z[,-1])),nrow=zrow,ncol=zcol)
if(is.null(dim(ys)) || ncol(ys) == 1) ys <- matrix(ys, 1, length(ys))
if(is.null(X0)) X0 <- matrix(1, ncol(ys), 1)
#handler of special Z and K
if(!is.null(Z)){ if(ncol(Z) == nrow(Z)) Z = NULL }
if(!is.null(K)) {if(length(K)<= 1) K = NULL}
X <- X0 #covariate variables such as population structure
j=1
if (is.null(Z)) Z=diag(x=1,nrow(K),ncol(K))
if (group==1) K=1
#print(head(X))
emma_test <- emmreml(as.numeric(ys), X=as.matrix(X), K=as.matrix(K), Z=Z,varbetahat=FALSE,varuhat=FALSE, PEVuhat=FALSE, test=FALSE)
print(paste(order_count, "of",numSetting,"--","Vg=",round(emma_test$Vu,4), "VE=",round(emma_test$Ve,4),"-2LL=",round(-2*emma_test$loglik,2), " Clustering=",ca," Group number=", group ," Group kinship=",kt,sep = " "))
emma_test_reml=-2*emma_test$loglik
storage_reml=append(storage_reml,-2*emma_test$loglik)
Compression[order_count,1]=kt
Compression[order_count,2]=ca
Compression[order_count,3]=group
Compression[order_count,4]=emma_test_reml
Compression[order_count,5]=emma_test$Vu
Compression[order_count,6]=emma_test$Ve
if(order_count==1){
save_remle=emma_test_reml
optimum_group=group
optimum_Clustering=ca
optimum_groupK=kt
}else{
if(emma_test_reml<save_remle){
save_remle=emma_test_reml
optimum_group=group
optimum_Clustering=ca
optimum_groupK=kt
}
}
} # kt end
} # ka end
} # group end
print(Compression)
if(optimum_group==1)
{
optimum_group=2
}
#print(colnames(KI)[53:62])
cp <- GAPIT.Compress(KI=KI,kinship.cluster=optimum_Clustering,kinship.group=optimum_groupK,GN=optimum_group,Timmer=Timmer,Memory=Memory)
bk <- GAPIT.Block(Z=hold_Z,GA=cp$GA,KG=cp$KG)
zc <- GAPIT.ZmatrixCompress(Z=hold_Z,GAU =bk$GA)
zrow=nrow(zc$Z)
zcol=ncol(zc$Z)-1
K = as.matrix(bk$KW)
Z=matrix(as.numeric(as.matrix(zc$Z[,-1])),nrow=zrow,ncol=zcol)
if(is.null(dim(ys)) || ncol(ys) == 1) ys <- matrix(ys, 1, length(ys))
if(is.null(X0)) X0 <- matrix(1, ncol(ys), 1)
X <- X0 #covariate variables such as population structure
if (is.null(Z)) Z=diag(x=1,nrow(K),ncol(K))
# print(my_allCV)
if (is.null(my_allCV)){my_allX=matrix(1,length(my_taxa),1)
}else{
# my_allX=as.matrix(my_allCV[,-1])
my_allX=cbind(1,as.matrix(my_allCV[,-1]))
}
emma_REMLE <- emmreml(y=as.numeric(ys), X=as.matrix(X), K=as.matrix(K), Z=Z,varbetahat=TRUE,varuhat=TRUE, PEVuhat=TRUE, test=TRUE)
#print(head(emma_REMLE$uhat))
#print(emma_REMLE$uhat[53:62])
emma_BLUE=as.matrix(my_allX)%*%as.matrix(emma_REMLE$betahat)
emma_BLUE=as.data.frame(cbind(my_taxa,emma_BLUE))
colnames(emma_BLUE)=c("Taxa","emma_BLUE")
gs <- GAPIT.GS(KW=bk$KW,KO=bk$KO,KWO=bk$KWO,GAU=bk$GAU,UW=cbind(emma_REMLE$uhat,emma_REMLE$PEVuhat))
#print(head(gs$BLUP))
#print(head(emma_BLUE))
BB= merge(gs$BLUP, emma_BLUE, by.x = "Taxa", by.y = "Taxa")
#print(head(BB))
prediction=as.matrix(BB$BLUP)+as.numeric(as.vector(BB$emma_BLUE))
all_gs=cbind(BB,prediction)
colnames(all_gs)=c("Taxa","Group","RefInf","ID","BLUP","PEV","BLUE","Prediction")
#print(head(all_gs))
#print(model)
write.csv(all_gs,paste("GAPIT.",model,".Pred.result.csv",sep=""), row.names = FALSE,col.names = TRUE)
print("GAPIT SUPER GS completed successfully for multiple traits. Results are saved")
return (list(GPS=BB,Pred=all_gs,Compression=Compression,kinship=my_allKI,SUPER_kinship=SUPER_myKI,SUPER_GD=SUPER_optimum_GD ,PC=my_allCV,Timmer=Timmer,Memory=Memory,GWAS=NULL ))
}
`GAPIT.Specify` <-
function(GI=NULL,GP=NULL,bin.size=10000000,inclosure.size=NULL,MaxBP=1e10){
#Object: To get indicator (TURE or FALSE) for GI based on GP
#Straitegy
# 1.set bins for all snps in GP
# 2.keep the snp with smallest P value in each bin, record SNP ID
# 3.Search GI for SNP with SNP ID from above
# 4.return the position for SNP selected
#Input:
#GI: Data frame with three columns (SNP name, chr and base position)
#GP: Data frame with seven columns (SNP name, chr and base position, P, MAF,N,effect)
#Output:
#theIndex: a vector indicating if the SNPs in GI belong to QTN or not)
#Authors: Zhiwu Zhang
#Last update: September 24, 2011
##############################################################################################
#print("Specification in process...")
if(is.null(GP))return (list(index=NULL,BP=NULL))
#set inclosure bin in GP
#Create SNP ID: position+CHR*MaxBP
ID.GP=as.numeric(as.vector(GP[,3]))+as.numeric(as.vector(GP[,2]))*MaxBP
#Creat bin ID
bin.GP=floor(ID.GP/bin.size )
#Create a table with bin ID, SNP ID and p value (set 2nd and 3rd NA temporately)
binP=as.matrix(cbind(bin.GP,NA,NA,ID.GP,as.numeric(as.vector(GP[,4]))) )
n=nrow(binP)
#Sort the table by p value and then bin ID (e.g. sort p within bin ID)
binP=binP[order(as.numeric(as.vector(binP[,5]))),] #sort on P alue
binP=binP[order(as.numeric(as.vector(binP[,1]))),] #sort on bin
#set indicator (use 2nd 3rd columns)
binP[2:n,2]=binP[1:(n-1),1]
binP[1,2]=0 #set the first
binP[,3]= binP[,1]-binP[,2]
#Se representives of bins
ID.GP=binP[binP[,3]>0,]
#Choose the most influencial bins as estimated QTNs
#Handler of single row
if(is.null(dim(ID.GP))) ID.GP=matrix(ID.GP,1,length(ID.GP))
ID.GP=ID.GP[order(as.numeric(as.vector(ID.GP[,5]))),] #sort on P alue
#Handler of single row (again after reshape)
if(is.null(dim(ID.GP))) ID.GP=matrix(ID.GP,1,length(ID.GP))
index=!is.na(ID.GP[,4])
ID.GP=ID.GP[index,4] #must have chr and bp information, keep SNP ID only
num_bins=NULL
if(!is.null(inclosure.size) ) {
if(!is.na(inclosure.size)){
avaiable=min(inclosure.size,length(ID.GP))
#print("inclosure.size length(ID.GP) avaiable")
#print(inclosure.size)
#print(length(ID.GP))
num_bins=length(ID.GP) # create number of all bins
#print(avaiable)
if(avaiable==0){
ID.GP=-1
}else{
ID.GP=ID.GP[1:avaiable] #keep the top ones selected
}
#print("ID.GP")
#print(ID.GP)
#problem here ID.GP[1:0]==ID.GP[1:1]
}
}
#create index in GI
theIndex=NULL
if(!is.null(GI)){
ID.GI=as.numeric(as.vector(GI[,3]))+as.numeric(as.vector(GI[,2]))*MaxBP
#print("ID.GI")
#print(ID.GI)
theIndex=ID.GI %in% ID.GP
}
#print("Specification in process done")
myList=list(index=theIndex,CB=ID.GP)
return (list(index=theIndex,CB=ID.GP,num_bins=num_bins))
} #end of GAPIT.Specify
#=============================================================================================
`GAPIT.Table` <-
function(final.table = final.table, name.of.trait = name.of.trait,SNP.FDR=1){
#Object: Make and export a table of summary information from GWAS
#Output: A table summarizing GWAS results
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: May 10, 2011
##############################################################################################
#Filter SNPs by FDR
index=(final.table[,7]<=SNP.FDR)
final.table=final.table[index,]
#Export this summary table as an excel file
write.table(final.table, paste("GAPIT.", name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#print("GAPIT.Table accomplished successfully!")
} #GAPIT.Table ends here
#=============================================================================================
`GAPIT.Timmer` <-
function(Timmer=NULL,Infor){
#Object: To report current time
#Output: Timmer
#Authors: Zhiwu Zhang
# Last update: may 8, 2011
##############################################################################################
Time<- Sys.time()
if(is.null(Timmer)) {
Elapsed=0
Timmer=cbind(Infor,Time,Elapsed)
}else{
Elapsed=0
Timmer.current=cbind(Infor,Time,Elapsed)
Timmer=rbind(Timmer,Timmer.current)
Timmer[nrow(Timmer),3]=as.numeric(as.matrix(Timmer[nrow(Timmer),2]))-as.numeric(as.matrix(Timmer[nrow(Timmer)-1,2]))
}
#print(paste('Time used: ', Timmer[nrow(Timmer),3], ' seconds for ',Infor,sep="" ))
return (Timmer)
}#end of GAPIT.Timmer function
#=============================================================================================
`GAPIT.ZmatrixCompress` <-
function(Z,GAU){
#Object: To assign the fraction of a individual belonging to a group
#Output: Z
#Authors: Zhiwu Zhang
# Last update: April 14, 2011
##############################################################################################
#Extraction of GAU coresponding to Z, sort GAU rowwise to mach columns of Z, and make design matrix
#print("GAPIT.ZmatrixCompress")
#print(dim(Z))
#print(dim(GAU))
effect.Z=as.matrix(Z[1,-1])
effect.GAU=as.matrix(GAU[,1])
taxa=as.data.frame(Z[-1,1])
GAU0=GAU[effect.GAU%in%effect.Z,]
order.GAU=order(GAU0[,1])
GAU1 <- GAU0[order.GAU,]
#id.1=GAU1[which(GAU1[,3]==1),4]
id.1=GAU1[which(GAU1[,3]<2),4]
n=max(as.numeric(as.vector(id.1)))
x=as.numeric(as.matrix(GAU1[,4]))
DS=diag(n)[x,]
#sort Z column wise
order.Z=order(effect.Z)
Z=Z[-1,-1]
Z <- Z[,order.Z]
#Z matrix from individual to group
#Z1.numeric <- as.numeric(as.matrix(Z))
Z <- matrix(as.numeric(as.matrix(Z)), nrow = nrow(Z), ncol = ncol(Z))
Z=Z%*%DS
#Z3=data.frame(cbind(as.character(Z[-1,1]),Z2))
Z=data.frame(cbind(taxa,Z))
#Z=Z3[order(Z3[,1]),]
Z=Z[order(as.matrix(taxa)),]
#print("GAPIT.ZmatrixCompress accomplished successfully!")
return(list(Z=Z))
}#The function GAPIT.ZmatrixCompress ends here
#=============================================================================================
`GAPIT.ZmatrixFormation` <-
function(Z,Y){
#Object: To expande the proportion Z to final Z
#Output: Z
#Authors: Zhiwu Zhang
# Last update: April 22, 2011
##############################################################################################
#split individuals in Y to the ones that are given Z and the one not
taxa.Z=as.matrix(Z[-1,1])
taxa.Y=as.matrix(Y[,1])
taxa.diff=setdiff(taxa.Y,taxa.Z)
taxa.I=as.matrix(taxa.Y[match(taxa.diff,taxa.Y,nomatch = 0)])
taxa.Z.col=as.matrix(Z[1,-1])
#Create final Z with zero block and identity block
Z0=matrix(data=0,nrow=nrow(taxa.Z),ncol=nrow(taxa.I))
Z1=diag(1,nrow(taxa.I))
ZC=as.matrix(rbind(Z0,Z1))
#To label rows and columns
label.row=rbind(as.matrix(Z[,1]),taxa.I)
label.col=t(taxa.I)
#update the zero block by the given Z matrix
position=t(as.matrix(match(taxa.Z.col,taxa.I,nomatch = 0)))
ZC[1:nrow(taxa.Z),position]=as.matrix(Z[-1,-1])
#habdler of parents do not have phenotype (colums of Z are not in taxa.I)
# To do list
#To form final Z matrix
dataPart=rbind(label.col,ZC)
Z=data.frame(cbind(label.row,dataPart))
#print("GAPIT.ZmatrixFormation accomplished successfully!")
return(Z)
}#The function GAPIT.ZmatrixFormation ends here
#=============================================================================================
`GAPIT.cross_validation.compare` <-function(myGD=NULL,y=NULL, rel=NULL,tc=NULL){
# Object: GAPIT.cross validation compare to different folders by replicate Times,result:a pdf of the scree barplot and .cvs
# myGD:numeric SNP
# Y: phenotype with columns of taxa,Y1,Y2...
# rel:replications
# tc:comparation folds number and value
# Authors: You Tang,Jiabo Wang and You Zhou
# Last update: December 31, 2014
##############################################################################################
if(is.null(myGD)||is.null(y)){stop("Validation Invalid. Please select read valid flies !")}
if(is.null(rel))
{
rel=10 #not input rel value,default replications number is 10
}
if(rel<2){stop("Validation Invalid. Please select replications >1 !")}
#rel<-2 ##replications
#t<-2
y<-y[!is.na(y[,2]),]
y<-y[,c(1,2)]
y<- na.omit(y)
#############
commonGeno <- unique(as.character(y[,1]))[unique(as.character(y[,1])) %in% myGD[,1]]
cG<-data.frame(commonGeno)
names(cG)<-"Taxa"
colnames(y)<-c("Taxa","pheno")
y2<-merge(y,cG,all.x=FALSE, all.y=TRUE, by = c("Taxa"))
Z1 <- myGD[match(y2$Taxa,myGD[,1]),]
myGD<- Z1
y<-y2
##############
X<-myGD[,-1]
k1<-as.matrix(X)
k2=GAPIT.kinship.VanRaden(snps=k1)
myKI<-as.data.frame(k2)
myKI<-cbind(myGD[,1],myKI)
write.table(y,"Y.txt",quote=F,sep="\t",row.names=F,col.names=T)
write.table(myKI,"K.txt",quote=F,row.names=F,col.names=F,sep="\t")
gc()
myK<- read.table("K.txt",head=F)
y= read.table("Y.txt",head=T)
y<- na.omit(y)
y=y[(y[,1] %in% myK[,1]),]
m=nrow(y)
if(is.null(tc))
tc<-c(2,5,10,20,50) ##default compare to folders num
tc1<-as.matrix(tc)
allstorage.ref=matrix(0,rel,nrow(tc1))
allstorage.inf=matrix(0,rel,nrow(tc1))
for(w in 1:nrow(tc1)){
num<-tc1[w,]
m.sample=floor(m/num)
storage.ref=matrix(0,rel,num)
storage.inf=matrix(0,rel,num)
#storage.REML=matrix(0,rel,num)
for(k in 1:rel)
{
#################Rand group method 1############
sets=sample(cut(1:nrow(y),num,labels=FALSE),nrow(y))
sets = as.data.frame(sets)
ynew <- cbind(sets,y)
#i=sample(1:num, size = 1)
for(i in 1:num){
#use only genotypes that were genotyped and phenotyped
ref <- y$Taxa[!ynew$sets==i]
lines.cali<- ref
# ycali<- y[match(ref,y$Taxa),]
#use only genotypes that were genotyped and phenotyped
test <- y$Taxa[ynew$sets==i]
lines.vali<-test
#yvali<- y[match(test,y$Taxa),]
#################end Rand group method############
#use only genotypes that were genotyped and phenotyped
commonGeno_v <- lines.vali[lines.vali %in% myK[,1]]
yvali<- y[match(commonGeno_v,y[,1]),]
#use only genotypes that were genotyped and phenotyped
commonGeno_c <- lines.cali[lines.cali %in% myK[,1]]
ycali<- y[match(commonGeno_c,y[,1]),]
Y.raw=ycali[,c(1,2)]#choos a trait
myY=Y.raw
myKI=myK
max.groups=m
#Run GAPIT
#############################################
myGAPIT <- GAPIT(
Y=myY,
KI=myKI,
#group.from=max.groups,
group.from=max.groups,
group.to=max.groups,
#group.by=10,
PCA.total=3,
SNP.test=FALSE,
file.output=FALSE
)
prediction=myGAPIT$Pred
prediction.ref<-prediction[match(commonGeno_c,prediction$Taxa),]
prediction.inf<-prediction[match(commonGeno_v,prediction$Taxa),]
YP.ref <- merge(y, prediction.ref, by.x = 1, by.y = "Taxa")
YP.inf <- merge(y, prediction.inf, by.x = 1, by.y = "Taxa")
#Calculate correlation and store them
r.ref=cor(as.numeric(as.vector(YP.ref[,2])),as.numeric(as.vector(YP.ref[,6]) ))
r.inf=cor(as.numeric(as.vector(YP.inf[,2])),as.numeric(as.vector(YP.inf[,6]) ))
if(r.inf<0){
#r.inf=cor(as.numeric(as.vector(YP.inf[,2])),as.numeric(as.vector(YP.inf[,2]+YP.inf[,6])))
combine_output=cbind(as.numeric(as.vector(YP.inf[,2])),as.numeric(as.vector(YP.inf[,6]) ))
write.csv(combine_output, paste("Accuracy_folders",num,k,i,rel,".csv",sep=""))
#stop("...........")
}
storage.ref[k,i]=r.ref
storage.inf[k,i]=r.inf
print(paste(" rel= ", rel, " k= ",k," i= ",i,sep = ""))
}
print(paste("finish replications k= ",k," folders= ",num,sep = ""))
}
#Find missing position-->0.0
index=is.na(storage.inf)
storage.inf[index]=0
allstorage.inf[,w]=as.matrix(rowMeans(storage.inf))
allstorage.ref[,w]=as.matrix(rowMeans(storage.ref))
#as.matrix(rowMeans(storage.ref))
##output rel times and accuracy for every folders
combine_output=cbind(storage.inf,allstorage.inf[,w])
combine_output1=cbind(storage.ref,allstorage.ref[,w])
colnames(combine_output)=c(paste("folders",c(1:num),sep=""),"mean")
write.csv(combine_output, paste("Accuracy_folders",num,"by CMLM,rel_",rel,".csv",sep=""))
write.csv(combine_output1, paste("Accuracy_folders ref",num,"by CMLM,rel_",rel,".csv",sep=""))
}
sr<-nrow(tc1)
##output means accuracy by rel for every folders
colnames(allstorage.inf)=c(paste(tc1[c(1:sr),]," folders",sep=""))
write.csv(allstorage.inf, paste("Accuracy_folders",nrow(tc1),"by CMLM,rel_",rel,".compare to means",".csv",sep=""))
write.csv(allstorage.ref, paste("Accuracy_folders ref",nrow(tc1),"by CMLM,rel_",rel,".compare to means",".csv",sep=""))
name.of.trait=noquote(names(Y.raw)[2])
#rrel=round(rel/2)
#ppp<-matrix(0,sr,2)
ppp<-matrix(0,sr,2)
#if(rrel!=1){
# aarm<-colMeans(allstorage.inf[1:rrel,])
# }else{
# aarm<-allstorage.inf[1,]
# }
#aam<-colMeans(allstorage.inf)
aam<-allstorage.inf
aam<-data.frame(aam)
bbm<-allstorage.ref
bbm<-data.frame(bbm)
for(b in 1:sr){
#ppp[b,]<-as.matrix(c(aarm[b],aam[b]))
ppp[b,1]<-as.matrix(mean(aam[,b]))
#colnames(ppp)<-c(rrel,rel)
}
for(c in 1:sr){
ppp[c,2]<-as.matrix(mean(bbm[,c]))
}
ppp<-as.matrix(cbind(ppp,tc1))
#colnames(ppp)<-c(rel)
sj<-runif(1, 0, 1)
#name.of.trait="qqq"
pdf(paste("GAPIT.cross_validation ", name.of.trait,sj,".compare to different folders.", ".pdf", sep = ""),width = 4.5, height = 4,pointsize=9)
par(mar = c(5,6,5,3))
palette(c("blue","red",rainbow(2)))
plot(ppp[,3],ppp[,2],xaxt="n",ylim=c(0,1.04),xlim=c(min(tc1)-1,max(tc1)+1),bg="lightgray",xlab="Number of folds",ylab="Correlation",type="o",pch=1,col=1,cex=1.0,cex.lab=1.7, cex.axis=1.3, lwd=3,las=1,lty =2)
axis(side=1,at=tc1,labels=tc1,cex.lab=1.7)
lines(ppp[,1]~ppp[,3], lwd=3,type="o",pch=19,col=2,lty =1)
legend("bottomright",horiz = FALSE,c("Reference","Inference"),pch = c(1,19), lty =c(2,1),col=c(1:2),lwd=2,cex=1.2,bty="n")
dev.off()
print(paste("GAPIT.cross validation ", name.of.trait,".compare to different folders.","successfully!" ,sep = ""))
return(list(allstorage.inf))
}#end GAPIT.cross validation compare to different folders by replicate Times
#=============================================================================================
emma.kinship <- function(snps, method="additive", use="all") {
n0 <- sum(snps==0,na.rm=TRUE)
nh <- sum(snps==0.5,na.rm=TRUE)
n1 <- sum(snps==1,na.rm=TRUE)
nNA <- sum(is.na(snps))
stopifnot(n0+nh+n1+nNA == length(snps))
if ( method == "dominant" ) {
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) > 0.5),nrow(snps),ncol(snps))
snps[!is.na(snps) && (snps == 0.5)] <- flags[!is.na(snps) && (snps == 0.5)]
}
else if ( method == "recessive" ) {
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) < 0.5),nrow(snps),ncol(snps))
snps[!is.na(snps) && (snps == 0.5)] <- flags[!is.na(snps) && (snps == 0.5)]
}
else if ( ( method == "additive" ) && ( nh > 0 ) ) {
dsnps <- snps
rsnps <- snps
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) > 0.5),nrow(snps),ncol(snps))
dsnps[!is.na(snps) && (snps==0.5)] <- flags[is.na(snps) && (snps==0.5)]
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) < 0.5),nrow(snps),ncol(snps))
rsnps[!is.na(snps) && (snps==0.5)] <- flags[is.na(snps) && (snps==0.5)]
snps <- rbind(dsnps,rsnps)
}
if ( use == "all" ) {
mafs <- matrix(rowMeans(snps,na.rm=TRUE),nrow(snps),ncol(snps))
snps[is.na(snps)] <- mafs[is.na(snps)]
}
else if ( use == "complete.obs" ) {
snps <- snps[rowSums(is.na(snps))==0,]
}
n <- ncol(snps)
K <- matrix(nrow=n,ncol=n)
diag(K) <- 1
for(i in 1:(n-1)) {
for(j in (i+1):n) {
x <- snps[,i]*snps[,j] + (1-snps[,i])*(1-snps[,j])
K[i,j] <- sum(x,na.rm=TRUE)/sum(!is.na(x))
K[j,i] <- K[i,j]
}
}
return(K)
}
emma.eigen.L <- function(Z,K,complete=TRUE) {
if ( is.null(Z) ) {
return(emma.eigen.L.wo.Z(K))
}
else {
return(emma.eigen.L.w.Z(Z,K,complete))
}
}
emma.eigen.L.wo.Z <- function(K) {
eig <- eigen(K,symmetric=TRUE)
return(list(values=eig$values,vectors=eig$vectors))
}
emma.eigen.L.w.Z <- function(Z,K,complete=TRUE) {
if ( complete == FALSE ) {
vids <- colSums(Z)>0
Z <- Z[,vids]
K <- K[vids,vids]
}
eig <- eigen(K%*%crossprod(Z,Z),symmetric=FALSE,EISPACK=TRUE)
return(list(values=eig$values,vectors=qr.Q(qr(Z%*%eig$vectors),complete=TRUE)))
}
emma.eigen.R <- function(Z,K,X,complete=TRUE) {
if ( is.null(Z) ) {
return(emma.eigen.R.wo.Z(K,X))
}
else {
return(emma.eigen.R.w.Z(Z,K,X,complete))
}
}
emma.eigen.R.wo.Z <- function(K, X) {
n <- nrow(X)
q <- ncol(X)
S <- diag(n)-X%*%solve(crossprod(X,X))%*%t(X)
eig <- eigen(S%*%(K+diag(1,n))%*%S,symmetric=TRUE)
stopifnot(!is.complex(eig$values))
return(list(values=eig$values[1:(n-q)]-1,vectors=eig$vectors[,1:(n-q)]))
}
emma.eigen.R.w.Z <- function(Z, K, X, complete = TRUE) {
if ( complete == FALSE ) {
vids <- colSums(Z) > 0
Z <- Z[,vids]
K <- K[vids,vids]
}
n <- nrow(Z)
t <- ncol(Z)
q <- ncol(X)
SZ <- Z - X%*%solve(crossprod(X,X))%*%crossprod(X,Z)
eig <- eigen(K%*%crossprod(Z,SZ),symmetric=FALSE,EISPACK=TRUE)
if ( is.complex(eig$values) ) {
eig$values <- Re(eig$values)
eig$vectors <- Re(eig$vectors)
}
qr.X <- qr.Q(qr(X))
return(list(values=eig$values[1:(t-q)],
vectors=qr.Q(qr(cbind(SZ%*%eig$vectors[,1:(t-q)],qr.X)),
complete=TRUE)[,c(1:(t-q),(t+1):n)]))
}
emma.delta.ML.LL.wo.Z <- function(logdelta, lambda, etas, xi) {
n <- length(xi)
delta <- exp(logdelta)
return( 0.5*(n*(log(n/(2*pi))-1-log(sum((etas*etas)/(lambda+delta))))-sum(log(xi+delta))) )
}
emma.delta.ML.LL.w.Z <- function(logdelta, lambda, etas.1, xi.1, n, etas.2.sq ) {
t <- length(xi.1)
delta <- exp(logdelta)
# stopifnot(length(lambda) == length(etas.1))
return( 0.5*(n*(log(n/(2*pi))-1-log(sum(etas.1*etas.1/(lambda+delta))+etas.2.sq/delta))-(sum(log(xi.1+delta))+(n-t)*logdelta)) )
}
emma.delta.ML.dLL.wo.Z <- function(logdelta, lambda, etas, xi) {
n <- length(xi)
delta <- exp(logdelta)
etasq <- etas*etas
ldelta <- lambda+delta
return( 0.5*(n*sum(etasq/(ldelta*ldelta))/sum(etasq/ldelta)-sum(1/(xi+delta))) )
}
emma.delta.ML.dLL.w.Z <- function(logdelta, lambda, etas.1, xi.1, n, etas.2.sq ) {
t <- length(xi.1)
q <- t-length(lambda)
delta <- exp(logdelta)
etasq <- etas.1*etas.1
ldelta <- lambda+delta
return( 0.5*(n*(sum(etasq/(ldelta*ldelta))+etas.2.sq/(delta*delta))/(sum(etasq/ldelta)+etas.2.sq/delta)-(sum(1/(xi.1+delta))+(n-t)/delta) ) )
}
emma.delta.REML.LL.wo.Z <- function(logdelta, lambda, etas) {
nq <- length(etas)
delta <- exp(logdelta)
return( 0.5*(nq*(log(nq/(2*pi))-1-log(sum(etas*etas/(lambda+delta))))-sum(log(lambda+delta))) )
}
emma.delta.REML.LL.w.Z <- function(logdelta, lambda, etas.1, n, t, etas.2.sq ) {
tq <- length(etas.1)
nq <- n - t + tq
delta <- exp(logdelta)
return( 0.5*(nq*(log(nq/(2*pi))-1-log(sum(etas.1*etas.1/(lambda+delta))+etas.2.sq/delta))-(sum(log(lambda+delta))+(n-t)*logdelta)) )
}
emma.delta.REML.dLL.wo.Z <- function(logdelta, lambda, etas) {
nq <- length(etas)
delta <- exp(logdelta)
etasq <- etas*etas
ldelta <- lambda+delta
return( 0.5*(nq*sum(etasq/(ldelta*ldelta))/sum(etasq/ldelta)-sum(1/ldelta)) )
}
emma.delta.REML.dLL.w.Z <- function(logdelta, lambda, etas.1, n, t1, etas.2.sq ) {
t <- t1
tq <- length(etas.1)
nq <- n - t + tq
delta <- exp(logdelta)
etasq <- etas.1*etas.1
ldelta <- lambda+delta
return( 0.5*(nq*(sum(etasq/(ldelta*ldelta))+etas.2.sq/(delta*delta))/(sum(etasq/ldelta)+etas.2.sq/delta)-(sum(1/ldelta)+(n-t)/delta)) )
}
emma.MLE <- function(y, X, K, Z=NULL, ngrids=100, llim=-10, ulim=10,
esp=1e-10, eig.L = NULL, eig.R = NULL)
{
n <- length(y)
t <- nrow(K)
q <- ncol(X)
# stopifnot(nrow(K) == t)
stopifnot(ncol(K) == t)
stopifnot(nrow(X) == n)
if ( det(crossprod(X,X)) == 0 ) {
warning("X is singular")
return (list(ML=0,delta=0,ve=0,vg=0))
}
if ( is.null(Z) ) {
if ( is.null(eig.L) ) {
eig.L <- emma.eigen.L.wo.Z(K)
}
if ( is.null(eig.R) ) {
eig.R <- emma.eigen.R.wo.Z(K,X)
}
etas <- crossprod(eig.R$vectors,y)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,n-q,m) + matrix(delta,n-q,m,byrow=TRUE)
Xis <- matrix(eig.L$values,n,m) + matrix(delta,n,m,byrow=TRUE)
Etasq <- matrix(etas*etas,n-q,m)
LL <- 0.5*(n*(log(n/(2*pi))-1-log(colSums(Etasq/Lambdas)))-colSums(log(Xis)))
dLL <- 0.5*delta*(n*colSums(Etasq/(Lambdas*Lambdas))/colSums(Etasq/Lambdas)-colSums(1/Xis))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if ( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.ML.LL.wo.Z(llim,eig.R$values,etas,eig.L$values))
}
if ( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.ML.LL.wo.Z(ulim,eig.R$values,etas,eig.L$values))
}
for( i in 1:(m-1) )
{
if ( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.ML.dLL.wo.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas=etas, xi=eig.L$values)
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.ML.LL.wo.Z(r$root,eig.R$values, etas, eig.L$values))
}
}
# optdelta <- exp(optlogdelta)
}
else {
if ( is.null(eig.L) ) {
eig.L <- emma.eigen.L.w.Z(Z,K)
}
if ( is.null(eig.R) ) {
eig.R <- emma.eigen.R.w.Z(Z,K,X)
}
etas <- crossprod(eig.R$vectors,y)
etas.1 <- etas[1:(t-q)]
etas.2 <- etas[(t-q+1):(n-q)]
etas.2.sq <- sum(etas.2*etas.2)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,t-q,m) + matrix(delta,t-q,m,byrow=TRUE)
Xis <- matrix(eig.L$values,t,m) + matrix(delta,t,m,byrow=TRUE)
Etasq <- matrix(etas.1*etas.1,t-q,m)
#LL <- 0.5*(n*(log(n/(2*pi))-1-log(colSums(Etasq/Lambdas)+etas.2.sq/delta))-colSums(log(Xis))+(n-t)*log(deltas))
dLL <- 0.5*delta*(n*(colSums(Etasq/(Lambdas*Lambdas))+etas.2.sq/(delta*delta))/(colSums(Etasq/Lambdas)+etas.2.sq/delta)-(colSums(1/Xis)+(n-t)/delta))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if ( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.ML.LL.w.Z(llim,eig.R$values,etas.1,eig.L$values,n,etas.2.sq))
}
if ( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.ML.LL.w.Z(ulim,eig.R$values,etas.1,eig.L$values,n,etas.2.sq))
}
for( i in 1:(m-1) )
{
if ( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.ML.dLL.w.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas.1=etas.1, xi.1=eig.L$values, n=n, etas.2.sq = etas.2.sq )
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.ML.LL.w.Z(r$root,eig.R$values, etas.1, eig.L$values, n, etas.2.sq ))
}
}
# optdelta <- exp(optlogdelta)
}
maxdelta <- exp(optlogdelta[which.max(optLL)])
maxLL <- max(optLL)
if ( is.null(Z) ) {
maxva <- sum(etas*etas/(eig.R$values+maxdelta))/n
}
else {
maxva <- (sum(etas.1*etas.1/(eig.R$values+maxdelta))+etas.2.sq/maxdelta)/n
}
maxve <- maxva*maxdelta
return (list(ML=maxLL,delta=maxdelta,ve=maxve,vg=maxva))
}
emma.REMLE <- function(y, X, K, Z=NULL, ngrids=100, llim=-10, ulim=10,
esp=1e-10, eig.L = NULL, eig.R = NULL) {
n <- length(y)
t <- nrow(K)
q <- ncol(X)
# stopifnot(nrow(K) == t)
stopifnot(ncol(K) == t)
stopifnot(nrow(X) == n)
if ( det(crossprod(X,X)) == 0 ) {
warning("X is singular")
return (list(REML=0,delta=0,ve=0,vg=0))
}
if ( is.null(Z) ) {
if ( is.null(eig.R) ) {
eig.R <- emma.eigen.R.wo.Z(K,X)
}
etas <- crossprod(eig.R$vectors,y)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,n-q,m) + matrix(delta,n-q,m,byrow=TRUE)
Etasq <- matrix(etas*etas,n-q,m)
LL <- 0.5*((n-q)*(log((n-q)/(2*pi))-1-log(colSums(Etasq/Lambdas)))-colSums(log(Lambdas)))
dLL <- 0.5*delta*((n-q)*colSums(Etasq/(Lambdas*Lambdas))/colSums(Etasq/Lambdas)-colSums(1/Lambdas))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if ( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(llim,eig.R$values,etas))
}
if ( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(ulim,eig.R$values,etas))
}
for( i in 1:(m-1) )
{
if ( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.REML.dLL.wo.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas=etas)
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(r$root,eig.R$values, etas))
}
}
# optdelta <- exp(optlogdelta)
}
else {
if ( is.null(eig.R) ) {
eig.R <- emma.eigen.R.w.Z(Z,K,X)
}
etas <- crossprod(eig.R$vectors,y)
etas.1 <- etas[1:(t-q)]
etas.2 <- etas[(t-q+1):(n-q)]
etas.2.sq <- sum(etas.2*etas.2)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,t-q,m) + matrix(delta,t-q,m,byrow=TRUE)
Etasq <- matrix(etas.1*etas.1,t-q,m)
dLL <- 0.5*delta*((n-q)*(colSums(Etasq/(Lambdas*Lambdas))+etas.2.sq/(delta*delta))/(colSums(Etasq/Lambdas)+etas.2.sq/delta)-(colSums(1/Lambdas)+(n-t)/delta))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if ( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(llim,eig.R$values,etas.1,n,t,etas.2.sq))
}
if ( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(ulim,eig.R$values,etas.1,n,t,etas.2.sq))
}
for( i in 1:(m-1) )
{
if ( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.REML.dLL.w.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas.1=etas.1, n=n, t1=t, etas.2.sq = etas.2.sq )
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(r$root,eig.R$values, etas.1, n, t, etas.2.sq ))
}
}
# optdelta <- exp(optlogdelta)
}
maxdelta <- exp(optlogdelta[which.max(optLL)])
maxLL <- max(optLL)
if ( is.null(Z) ) {
maxva <- sum(etas*etas/(eig.R$values+maxdelta))/(n-q)
}
else {
maxva <- (sum(etas.1*etas.1/(eig.R$values+maxdelta))+etas.2.sq/maxdelta)/(n-q)
}
maxve <- maxva*maxdelta
return (list(REML=maxLL,delta=maxdelta,ve=maxve,vg=maxva))
}
emma.ML.LRT <- function(ys, xs, K, Z=NULL, X0 = NULL, ngrids=100, llim=-10, ulim=10, esp=1e-10, ponly = FALSE) {
if ( is.null(dim(ys)) || ncol(ys) == 1 ) {
ys <- matrix(ys,1,length(ys))
}
if ( is.null(dim(xs)) || ncol(xs) == 1 ) {
xs <- matrix(xs,1,length(xs))
}
if ( is.null(X0) ) {
X0 <- matrix(1,ncol(ys),1)
}
g <- nrow(ys)
n <- ncol(ys)
m <- nrow(xs)
t <- ncol(xs)
q0 <- ncol(X0)
q1 <- q0 + 1
if ( !ponly ) {
ML1s <- matrix(nrow=m,ncol=g)
ML0s <- matrix(nrow=m,ncol=g)
vgs <- matrix(nrow=m,ncol=g)
ves <- matrix(nrow=m,ncol=g)
}
stats <- matrix(nrow=m,ncol=g)
ps <- matrix(nrow=m,ncol=g)
ML0 <- vector(length=g)
stopifnot(nrow(K) == t)
stopifnot(ncol(K) == t)
stopifnot(nrow(X0) == n)
if ( sum(is.na(ys)) == 0 ) {
eig.L <- emma.eigen.L(Z,K)
eig.R0 <- emma.eigen.R(Z,K,X0)
for(i in 1:g) {
ML0[i] <- emma.MLE(ys[i,],X0,K,Z,ngrids,llim,ulim,esp,eig.L,eig.R0)$ML
}
x.prev <- vector(length=0)
for(i in 1:m) {
vids <- !is.na(xs[i,])
nv <- sum(vids)
xv <- xs[i,vids]
if ( ( mean(xv) <= 0 ) || ( mean(xv) >= 1 ) ) {
if (!ponly) {
stats[i,] <- rep(NA,g)
vgs[i,] <- rep(NA,g)
ves[i,] <- rep(NA,g)
ML1s[i,] <- rep(NA,g)
ML0s[i,] <- rep(NA,g)
}
ps[i,] = rep(1,g)
}
else if ( identical(x.prev, xv) ) {
if ( !ponly ) {
stats[i,] <- stats[i-1,]
vgs[i,] <- vgs[i-1,]
ves[i,] <- ves[i-1,]
ML1s[i,] <- ML1s[i-1,]
ML0s[i,] <- ML0s[i-1,]
}
ps[i,] <- ps[i-1,]
}
else {
if ( is.null(Z) ) {
X <- cbind(X0[vids,,drop=FALSE],xs[i,vids])
eig.R1 = emma.eigen.R.wo.Z(K[vids,vids],X)
}
else {
vrows <- as.logical(rowSums(Z[,vids]))
nr <- sum(vrows)
X <- cbind(X0[vrows,,drop=FALSE],Z[vrows,vids]%*%t(xs[i,vids,drop=FALSE]))
eig.R1 = emma.eigen.R.w.Z(Z[vrows,vids],K[vids,vids],X)
}
for(j in 1:g) {
if ( nv == t ) {
MLE <- emma.MLE(ys[j,],X,K,Z,ngrids,llim,ulim,esp,eig.L,eig.R1)
# MLE <- emma.MLE(ys[j,],X,K,Z,ngrids,llim,ulim,esp,eig.L,eig.R1)
if (!ponly) {
ML1s[i,j] <- MLE$ML
vgs[i,j] <- MLE$vg
ves[i,j] <- MLE$ve
}
stats[i,j] <- 2*(MLE$ML-ML0[j])
}
else {
if ( is.null(Z) ) {
eig.L0 <- emma.eigen.L.wo.Z(K[vids,vids])
MLE0 <- emma.MLE(ys[j,vids],X0[vids,,drop=FALSE],K[vids,vids],NULL,ngrids,llim,ulim,esp,eig.L0)
MLE1 <- emma.MLE(ys[j,vids],X,K[vids,vids],NULL,ngrids,llim,ulim,esp,eig.L0)
}
else {
if ( nr == n ) {
MLE1 <- emma.MLE(ys[j,],X,K,Z,ngrids,llim,ulim,esp,eig.L)
}
else {
eig.L0 <- emma.eigen.L.w.Z(Z[vrows,vids],K[vids,vids])
MLE0 <- emma.MLE(ys[j,vrows],X0[vrows,,drop=FALSE],K[vids,vids],Z[vrows,vids],ngrids,llim,ulim,esp,eig.L0)
MLE1 <- emma.MLE(ys[j,vrows],X,K[vids,vids],Z[vrows,vids],ngrids,llim,ulim,esp,eig.L0)
}
}
if (!ponly) {
ML1s[i,j] <- MLE1$ML
ML0s[i,j] <- MLE0$ML
vgs[i,j] <- MLE1$vg
ves[i,j] <- MLE1$ve
}
stats[i,j] <- 2*(MLE1$ML-MLE0$ML)
}
}
if ( ( nv == t ) && ( !ponly ) ) {
ML0s[i,] <- ML0
}
ps[i,] <- pchisq(stats[i,],1,lower.tail=FALSE)
}
}
}
else {
eig.L <- emma.eigen.L(Z,K)
eig.R0 <- emma.eigen.R(Z,K,X0)
for(i in 1:g) {
vrows <- !is.na(ys[i,])
if ( is.null(Z) ) {
ML0[i] <- emma.MLE(ys[i,vrows],X0[vrows,,drop=FALSE],K[vrows,vrows],NULL,ngrids,llim,ulim,esp)$ML
}
else {
vids <- colSums(Z[vrows,]>0)
ML0[i] <- emma.MLE(ys[i,vrows],X0[vrows,,drop=FALSE],K[vids,vids],Z[vrows,vids],ngrids,llim,ulim,esp)$ML
}
}
x.prev <- vector(length=0)
for(i in 1:m) {
vids <- !is.na(xs[i,])
nv <- sum(vids)
xv <- xs[i,vids]
if ( ( mean(xv) <= 0 ) || ( mean(xv) >= 1 ) ) {
if (!ponly) {
stats[i,] <- rep(NA,g)
vgs[i,] <- rep(NA,g)
ves[i,] <- rep(NA,g)
ML1s[i,] <- rep(NA,g)
ML0s[,i] <- rep(NA,g)
}
ps[i,] = rep(1,g)
}
else if ( identical(x.prev, xv) ) {
if ( !ponly ) {
stats[i,] <- stats[i-1,]
vgs[i,] <- vgs[i-1,]
ves[i,] <- ves[i-1,]
ML1s[i,] <- ML1s[i-1,]
}
ps[i,] = ps[i-1,]
}
else {
if ( is.null(Z) ) {
X <- cbind(X0,xs[i,])
if ( nv == t ) {
eig.R1 = emma.eigen.R.wo.Z(K,X)
}
}
else {
vrows <- as.logical(rowSums(Z[,vids]))
X <- cbind(X0,Z[,vids,drop=FALSE]%*%t(xs[i,vids,drop=FALSE]))
if ( nv == t ) {
eig.R1 = emma.eigen.R.w.Z(Z,K,X)
}
}
for(j in 1:g) {
# print(j)
vrows <- !is.na(ys[j,])
if ( nv == t ) {
nr <- sum(vrows)
if ( is.null(Z) ) {
if ( nr == n ) {
MLE <- emma.MLE(ys[j,],X,K,NULL,ngrids,llim,ulim,esp,eig.L,eig.R1)
}
else {
MLE <- emma.MLE(ys[j,vrows],X[vrows,],K[vrows,vrows],NULL,ngrids,llim,ulim,esp)
}
}
else {
if ( nr == n ) {
MLE <- emma.MLE(ys[j,],X,K,Z,ngrids,llim,ulim,esp,eig.L,eig.R1)
}
else {
vtids <- as.logical(colSums(Z[vrows,,drop=FALSE]))
MLE <- emma.MLE(ys[j,vrows],X[vrows,],K[vtids,vtids],Z[vrows,vtids],ngrids,llim,ulim,esp)
}
}
if (!ponly) {
ML1s[i,j] <- MLE$ML
vgs[i,j] <- MLE$vg
ves[i,j] <- MLE$ve
}
stats[i,j] <- 2*(MLE$ML-ML0[j])
}
else {
if ( is.null(Z) ) {
vtids <- vrows & vids
eig.L0 <- emma.eigen.L(NULL,K[vtids,vtids])
MLE0 <- emma.MLE(ys[j,vtids],X0[vtids,,drop=FALSE],K[vtids,vtids],NULL,ngrids,llim,ulim,esp,eig.L0)
MLE1 <- emma.MLE(ys[j,vtids],X[vtids,],K[vtids,vtids],NULL,ngrids,llim,ulim,esp,eig.L0)
}
else {
vtids <- as.logical(colSums(Z[vrows,])) & vids
vtrows <- vrows & as.logical(rowSums(Z[,vids]))
eig.L0 <- emma.eigen.L(Z[vtrows,vtids],K[vtids,vtids])
MLE0 <- emma.MLE(ys[j,vtrows],X0[vtrows,,drop=FALSE],K[vtids,vtids],Z[vtrows,vtids],ngrids,llim,ulim,esp,eig.L0)
MLE1 <- emma.MLE(ys[j,vtrows],X[vtrows,],K[vtids,vtids],Z[vtrows,vtids],ngrids,llim,ulim,esp,eig.L0)
}
if (!ponly) {
ML1s[i,j] <- MLE1$ML
vgs[i,j] <- MLE1$vg
ves[i,j] <- MLE1$ve
ML0s[i,j] <- MLE0$ML
}
stats[i,j] <- 2*(MLE1$ML-MLE0$ML)
}
}
if ( ( nv == t ) && ( !ponly ) ) {
ML0s[i,] <- ML0
}
ps[i,] <- pchisq(stats[i,],1,lower.tail=FALSE)
}
}
}
if ( ponly ) {
return (ps)
}
else {
return (list(ps=ps,ML1s=ML1s,ML0s=ML0s,stats=stats,vgs=vgs,ves=ves))
}
}
emma.REML.t <- function(ys, xs, K, Z=NULL, X0 = NULL, ngrids=100, llim=-10, ulim=10, esp=1e-10, ponly = FALSE) {
if ( is.null(dim(ys)) || ncol(ys) == 1 ) {
ys <- matrix(ys,1,length(ys))
}
if ( is.null(dim(xs)) || ncol(xs) == 1 ) {
xs <- matrix(xs,1,length(xs))
}
if ( is.null(X0) ) {
X0 <- matrix(1,ncol(ys),1)
}
g <- nrow(ys)
n <- ncol(ys)
m <- nrow(xs)
t <- ncol(xs)
q0 <- ncol(X0)
q1 <- q0 + 1
stopifnot(nrow(K) == t)
stopifnot(ncol(K) == t)
stopifnot(nrow(X0) == n)
if ( !ponly ) {
REMLs <- matrix(nrow=m,ncol=g)
vgs <- matrix(nrow=m,ncol=g)
ves <- matrix(nrow=m,ncol=g)
}
dfs <- matrix(nrow=m,ncol=g)
stats <- matrix(nrow=m,ncol=g)
ps <- matrix(nrow=m,ncol=g)
if ( sum(is.na(ys)) == 0 ) {
eig.L <- emma.eigen.L(Z,K)
x.prev <- vector(length=0)
for(i in 1:m) {
vids <- !is.na(xs[i,])
nv <- sum(vids)
xv <- xs[i,vids]
if ( ( mean(xv) <= 0 ) || ( mean(xv) >= 1 ) ) {
if ( !ponly ) {
vgs[i,] <- rep(NA,g)
ves[i,] <- rep(NA,g)
dfs[i,] <- rep(NA,g)
REMLs[i,] <- rep(NA,g)
stats[i,] <- rep(NA,g)
}
ps[i,] = rep(1,g)
}
else if ( identical(x.prev, xv) ) {
if ( !ponly ) {
vgs[i,] <- vgs[i-1,]
ves[i,] <- ves[i-1,]
dfs[i,] <- dfs[i-1,]
REMLs[i,] <- REMLs[i-1,]
stats[i,] <- stats[i-1,]
}
ps[i,] <- ps[i-1,]
}
else {
if ( is.null(Z) ) {
X <- cbind(X0[vids,,drop=FALSE],xs[i,vids])
eig.R1 = emma.eigen.R.wo.Z(K[vids,vids],X)
}
else {
vrows <- as.logical(rowSums(Z[,vids]))
X <- cbind(X0[vrows,,drop=FALSE],Z[vrows,vids,drop=FALSE]%*%t(xs[i,vids,drop=FALSE]))
eig.R1 = emma.eigen.R.w.Z(Z[vrows,vids],K[vids,vids],X)
}
for(j in 1:g) {
if ( nv == t ) {
REMLE <- emma.REMLE(ys[j,],X,K,Z,ngrids,llim,ulim,esp,eig.R1)
if ( is.null(Z) ) {
U <- eig.L$vectors * matrix(sqrt(1/(eig.L$values+REMLE$delta)),t,t,byrow=TRUE)
dfs[i,j] <- nv - q1
}
else {
U <- eig.L$vectors * matrix(c(sqrt(1/(eig.L$values+REMLE$delta)),rep(sqrt(1/REMLE$delta),n-t)),n,n,byrow=TRUE)
dfs[i,j] <- n - q1
}
yt <- crossprod(U,ys[j,])
Xt <- crossprod(U,X)
iXX <- solve(crossprod(Xt,Xt))
beta <- iXX%*%crossprod(Xt,yt)
if ( !ponly ) {
vgs[i,j] <- REMLE$vg
ves[i,j] <- REMLE$ve
REMLs[i,j] <- REMLE$REML
}
stats[i,j] <- beta[q1]/sqrt(iXX[q1,q1]*REMLE$vg)
}
else {
if ( is.null(Z) ) {
eig.L0 <- emma.eigen.L.wo.Z(K[vids,vids])
nr <- sum(vids)
yv <- ys[j,vids]
REMLE <- emma.REMLE(yv,X,K[vids,vids,drop=FALSE],NULL,ngrids,llim,ulim,esp,eig.R1)
U <- eig.L0$vectors * matrix(sqrt(1/(eig.L0$values+REMLE$delta)),nr,nr,byrow=TRUE)
dfs[i,j] <- nr - q1
}
else {
eig.L0 <- emma.eigen.L.w.Z(Z[vrows,vids,drop=FALSE],K[vids,vids])
yv <- ys[j,vrows]
nr <- sum(vrows)
tv <- sum(vids)
REMLE <- emma.REMLE(yv,X,K[vids,vids,drop=FALSE],Z[vrows,vids,drop=FALSE],ngrids,llim,ulim,esp,eig.R1)
U <- eig.L0$vectors * matrix(c(sqrt(1/(eig.L0$values+REMLE$delta)),rep(sqrt(1/REMLE$delta),nr-tv)),nr,nr,byrow=TRUE)
dfs[i,j] <- nr - q1
}
yt <- crossprod(U,yv)
Xt <- crossprod(U,X)
iXX <- solve(crossprod(Xt,Xt))
beta <- iXX%*%crossprod(Xt,yt)
if (!ponly) {
vgs[i,j] <- REMLE$vg
ves[i,j] <- REMLE$ve
REMLs[i,j] <- REMLE$REML
}
stats[i,j] <- beta[q1]/sqrt(iXX[q1,q1]*REMLE$vg)
}
}
ps[i,] <- 2*pt(abs(stats[i,]),dfs[i,],lower.tail=FALSE)
}
}
}
else {
eig.L <- emma.eigen.L(Z,K)
eig.R0 <- emma.eigen.R(Z,K,X0)
x.prev <- vector(length=0)
for(i in 1:m) {
vids <- !is.na(xs[i,])
nv <- sum(vids)
xv <- xs[i,vids]
if ( ( mean(xv) <= 0 ) || ( mean(xv) >= 1 ) ) {
if (!ponly) {
vgs[i,] <- rep(NA,g)
ves[i,] <- rep(NA,g)
REMLs[i,] <- rep(NA,g)
dfs[i,] <- rep(NA,g)
}
ps[i,] = rep(1,g)
}
else if ( identical(x.prev, xv) ) {
if ( !ponly ) {
stats[i,] <- stats[i-1,]
vgs[i,] <- vgs[i-1,]
ves[i,] <- ves[i-1,]
REMLs[i,] <- REMLs[i-1,]
dfs[i,] <- dfs[i-1,]
}
ps[i,] = ps[i-1,]
}
else {
if ( is.null(Z) ) {
X <- cbind(X0,xs[i,])
if ( nv == t ) {
eig.R1 = emma.eigen.R.wo.Z(K,X)
}
}
else {
vrows <- as.logical(rowSums(Z[,vids,drop=FALSE]))
X <- cbind(X0,Z[,vids,drop=FALSE]%*%t(xs[i,vids,drop=FALSE]))
if ( nv == t ) {
eig.R1 = emma.eigen.R.w.Z(Z,K,X)
}
}
for(j in 1:g) {
vrows <- !is.na(ys[j,])
if ( nv == t ) {
yv <- ys[j,vrows]
nr <- sum(vrows)
if ( is.null(Z) ) {
if ( nr == n ) {
REMLE <- emma.REMLE(yv,X,K,NULL,ngrids,llim,ulim,esp,eig.R1)
U <- eig.L$vectors * matrix(sqrt(1/(eig.L$values+REMLE$delta)),n,n,byrow=TRUE)
}
else {
eig.L0 <- emma.eigen.L.wo.Z(K[vrows,vrows,drop=FALSE])
REMLE <- emma.REMLE(yv,X[vrows,,drop=FALSE],K[vrows,vrows,drop=FALSE],NULL,ngrids,llim,ulim,esp)
U <- eig.L0$vectors * matrix(sqrt(1/(eig.L0$values+REMLE$delta)),nr,nr,byrow=TRUE)
}
dfs[i,j] <- nr-q1
}
else {
if ( nr == n ) {
REMLE <- emma.REMLE(yv,X,K,Z,ngrids,llim,ulim,esp,eig.R1)
U <- eig.L$vectors * matrix(c(sqrt(1/(eig.L$values+REMLE$delta)),rep(sqrt(1/REMLE$delta),n-t)),n,n,byrow=TRUE)
}
else {
vtids <- as.logical(colSums(Z[vrows,,drop=FALSE]))
eig.L0 <- emma.eigen.L.w.Z(Z[vrows,vtids,drop=FALSE],K[vtids,vtids,drop=FALSE])
REMLE <- emma.REMLE(yv,X[vrows,,drop=FALSE],K[vtids,vtids,drop=FALSE],Z[vrows,vtids,drop=FALSE],ngrids,llim,ulim,esp)
U <- eig.L0$vectors * matrix(c(sqrt(1/(eig.L0$values+REMLE$delta)),rep(sqrt(1/REMLE$delta),nr-sum(vtids))),nr,nr,byrow=TRUE)
}
dfs[i,j] <- nr-q1
}
yt <- crossprod(U,yv)
Xt <- crossprod(U,X[vrows,,drop=FALSE])
iXX <- solve(crossprod(Xt,Xt))
beta <- iXX%*%crossprod(Xt,yt)
if ( !ponly ) {
vgs[i,j] <- REMLE$vg
ves[i,j] <- REMLE$ve
REMLs[i,j] <- REMLE$REML
}
stats[i,j] <- beta[q1]/sqrt(iXX[q1,q1]*REMLE$vg)
}
else {
if ( is.null(Z) ) {
vtids <- vrows & vids
eig.L0 <- emma.eigen.L.wo.Z(K[vtids,vtids,drop=FALSE])
yv <- ys[j,vtids]
nr <- sum(vtids)
REMLE <- emma.REMLE(yv,X[vtids,,drop=FALSE],K[vtids,vtids,drop=FALSE],NULL,ngrids,llim,ulim,esp)
U <- eig.L0$vectors * matrix(sqrt(1/(eig.L0$values+REMLE$delta)),nr,nr,byrow=TRUE)
Xt <- crossprod(U,X[vtids,,drop=FALSE])
dfs[i,j] <- nr-q1
}
else {
vtids <- as.logical(colSums(Z[vrows,,drop=FALSE])) & vids
vtrows <- vrows & as.logical(rowSums(Z[,vids,drop=FALSE]))
eig.L0 <- emma.eigen.L.w.Z(Z[vtrows,vtids,drop=FALSE],K[vtids,vtids,drop=FALSE])
yv <- ys[j,vtrows]
nr <- sum(vtrows)
REMLE <- emma.REMLE(yv,X[vtrows,,drop=FALSE],K[vtids,vtids,drop=FALSE],Z[vtrows,vtids,drop=FALSE],ngrids,llim,ulim,esp)
U <- eig.L0$vectors * matrix(c(sqrt(1/(eig.L0$values+REMLE$delta)),rep(sqrt(1/REMLE$delta),nr-sum(vtids))),nr,nr,byrow=TRUE)
Xt <- crossprod(U,X[vtrows,,drop=FALSE])
dfs[i,j] <- nr-q1
}
yt <- crossprod(U,yv)
iXX <- solve(crossprod(Xt,Xt))
beta <- iXX%*%crossprod(Xt,yt)
if ( !ponly ) {
vgs[i,j] <- REMLE$vg
ves[i,j] <- REMLE$ve
REMLs[i,j] <- REMLE$REML
}
stats[i,j] <- beta[q1]/sqrt(iXX[q1,q1]*REMLE$vg)
}
}
ps[i,] <- 2*pt(abs(stats[i,]),dfs[i,],lower.tail=FALSE)
}
}
}
if ( ponly ) {
return (ps)
}
else {
return (list(ps=ps,REMLs=REMLs,stats=stats,dfs=dfs,vgs=vgs,ves=ves))
}
}
`GAPIT.emma.REMLE` <-
function(y, X, K, Z=NULL, ngrids=100, llim=-10, ulim=10,
esp=1e-10, eig.L = NULL, eig.R = NULL) {
# Authors: Hyun Min Kang
# Modified (only one line) by Zhiwu Zhang to handle non-defined LL ("NaN") by replacing it with the worst LL.
# Last update: June 8, 2011
##############################################################################################
n <- length(y)
t <- nrow(K)
q <- ncol(X)
# stopifnot(nrow(K) == t)
stopifnot(ncol(K) == t)
stopifnot(nrow(X) == n)
if( det(crossprod(X,X)) == 0 ) {
warning("X is singular")
return (list(REML=0,delta=0,ve=0,vg=0))
}
if(is.null(Z) ) {
if(is.null(eig.R) ) {
eig.R <- emma.eigen.R.wo.Z(K,X)
}
etas <- crossprod(eig.R$vectors,y)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,n-q,m) + matrix(delta,n-q,m,byrow=TRUE)
Etasq <- matrix(etas*etas,n-q,m)
LL <- 0.5*((n-q)*(log((n-q)/(2*pi))-1-log(colSums(Etasq/Lambdas)))-colSums(log(Lambdas)))
dLL <- 0.5*delta*((n-q)*colSums(Etasq/(Lambdas*Lambdas))/colSums(Etasq/Lambdas)-colSums(1/Lambdas))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(llim,eig.R$values,etas))
}
if( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(ulim,eig.R$values,etas))
}
for(i in 1:(m-1) )
{
if( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.REML.dLL.wo.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas=etas)
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(r$root,eig.R$values, etas))
}
}
# optdelta <- exp(optlogdelta)
}
else {
if(is.null(eig.R) ) {
eig.R <- emma.eigen.R.w.Z(Z,K,X)
}
etas <- crossprod(eig.R$vectors,y)
etas.1 <- etas[1:(t-q)]
etas.2 <- etas[(t-q+1):(n-q)]
etas.2.sq <- sum(etas.2*etas.2)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,t-q,m) + matrix(delta,t-q,m,byrow=TRUE)
Etasq <- matrix(etas.1*etas.1,t-q,m)
dLL <- 0.5*delta*((n-q)*(colSums(Etasq/(Lambdas*Lambdas))+etas.2.sq/(delta*delta))/(colSums(Etasq/Lambdas)+etas.2.sq/delta)-(colSums(1/Lambdas)+(n-t)/delta))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(llim,eig.R$values,etas.1,n,t,etas.2.sq))
}
if( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(ulim,eig.R$values,etas.1,n,t,etas.2.sq))
}
for(i in 1:(m-1) )
{
if( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.REML.dLL.w.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas.1=etas.1, n=n, t1=t, etas.2.sq = etas.2.sq )
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(r$root,eig.R$values, etas.1, n, t, etas.2.sq ))
}
}
# optdelta <- exp(optlogdelta)
}
maxdelta <- exp(optlogdelta[which.max(optLL)])
#handler of grids with NaN log
optLL=GAPIT.replaceNaN(optLL)
maxLL <- max(optLL)
if(is.null(Z) ) {
maxva <- sum(etas*etas/(eig.R$values+maxdelta))/(n-q)
}
else {
maxva <- (sum(etas.1*etas.1/(eig.R$values+maxdelta))+etas.2.sq/maxdelta)/(n-q)
}
maxve <- maxva*maxdelta
return (list(REML=maxLL,delta=maxdelta,ve=maxve,vg=maxva))
}
#=============================================================================================
`GAPIT.get.LL` <-
compiler::cmpfun(
function(pheno,geno=NULL,snp.pool,X0=NULL){
# evaluation of the maximum likelihood
#Input: ys, xs, vg, delta, Z, X0, snp.pool
#Output: LL
#Authors: Qishan Wang, Feng Tian and Zhiwu Zhang
#Last update: April 16, 2012
################################################################################
#print("GAPIT.get.LL started")
#print("dimension of pheno, snpool and X0")
#print(dim(pheno))
#print(length(pheno))
#print(dim(snp.pool))
#print(length(snp.pool))
#print(dim(X0))
#print(length(X0))
y=pheno
p=0
deltaExpStart = -5
deltaExpEnd = 5
snp.pool=snp.pool[,]
if(!is.null(snp.pool)&&var(snp.pool)==0){
deltaExpStart = 100
deltaExpEnd = deltaExpStart
#print("deltaExp change here")
}
if(is.null(X0)) {
X0 = matrix(1, nrow(snp.pool), 1)
}
#snp.test=as.numeric(geno[,1])
#X <- cbind(X0, snp.test)
X=X0
#########SVD of X
K.X.svd= svd(snp.pool,LINPACK=TRUE)######rivised by Jiabo Wang 2016.1.8
# snp.pool=NA problem occurred
#####rivised 2012.4.15 by qishan wang
d=K.X.svd$d
d=d[d>1e-08]
d=d^2
U1=K.X.svd$u
U1=U1[,1:length(d)] ##rivised 2012.4.15 by qishan wang
#handler of single snp
if(is.null(dim(U1))) U1=matrix(U1,ncol=1)
###################
n=nrow(U1)
#I= diag(1,nrow(U1)) #xiaolei removed, this costs lots of memory
U1TX=crossprod(U1,X)
U1TY=crossprod(U1,y)
yU1TY<- y-U1%*%U1TY
XU1TX<- X-U1%*%U1TX ### i is out of bracket
#xiaolei rewrite following 4 lines
IU = -tcrossprod(U1,U1)
diag(IU) = rep(1,n) + diag(IU)
#IUU=(I-tcrossprod(U1,U1))
IUX=crossprod(IU,X )
IUY=crossprod(IU,y)
#Iteration on the range of delta (-5 to 5 in glog scale)
for (m in seq(deltaExpStart,deltaExpEnd,by=0.1))
{
p=p+1
delta<- exp(m)
#----------------------------calculate beta-------------------------------------
#######get beta compnents 1
beta1=0
for(i in 1:length(d)){
one=matrix(U1TX[i,], nrow=1)
beta=crossprod(one,(one/(d[i]+delta))) #This is not real beta, confusing
beta1= beta1+beta
}
#######get beta components 2
beta2=0
for(i in 1:nrow(U1)){
one=matrix(IUX[i,], nrow=1)
dim(one)
beta=crossprod(one,one)
beta2= beta2+beta
}
beta2<-beta2/delta
#######get b3
beta3=0
for(i in 1:length(d)){
one1=matrix(U1TX[i,], nrow=1)
one2=matrix(U1TY[i,], nrow=1)
beta=crossprod(one1,(one2/(d[i]+delta))) #This is not real beta, confusing
beta3= beta3+beta
}
###########get beta4
beta4=0
for(i in 1:nrow(U1)){
one1=matrix(IUX[i,], nrow=1)
one2=matrix(IUY[i,], nrow=1)
beta=crossprod(one1,one2) #This is not real beta, confusing
beta4= beta4+beta
}
beta4<-beta4/delta
#######get final beta
#zw1=solve(beta1+beta2)
zw1 <- try(solve(beta1+beta2),silent=TRUE)
if(inherits(zw1, "try-error")){
zw1 <- ginv(beta1+beta2)
}
#zw1=ginv(beta1+beta2)
zw2=(beta3+beta4)
beta=crossprod(zw1,zw2) #This is the real beta
#----------------------------calculate LL---------------------------------------
####part 1
part11<-n*log(2*3.14)
part12<-0
for(i in 1:length(d)){
part12_pre=log(d[i]+delta)
part12= part12+part12_pre
}
part13<- (nrow(U1)-length(d))*log(delta)
part1<- -1/2*(part11+part12+part13)
###### part2
part21<-nrow(U1)
######part221
part221=0
for(i in 1:length(d)){
one1=matrix(U1TX[i,], nrow=1)
one2=matrix(U1TY[i,], nrow=1)
part221_pre=(one2-one1%*%beta)^2/(d[i]+delta) ###### beta contain covariate and snp %*%
part221= part221+part221_pre
}
######part222
part222=0
for(i in 1:n){
one1=matrix(XU1TX[i,], nrow=1)
one2=matrix(yU1TY[i,], nrow=1)
part222_pre=((one2-one1%*%beta)^2)/delta
part222= part222+part222_pre
}
part22<-n*log((1/n)*(part221+part222))
part2<- -1/2*(part21+part22)
################# likihood
LL<-part1+part2
part1<-0
part2<-0
#-----------------------Save the optimum---------------------------------------
if(p==1){
beta.save=beta
delta.save=delta
LL.save=LL
}else{
if(LL>LL.save){
beta.save=beta
delta.save=delta
LL.save=LL
}
}
} # end of Iteration on the range of delta (-5 to 5 in glog scale)
#--------------------update with the optimum------------------------------------
beta=beta.save
delta=delta.save
LL=LL.save
names(delta)=NULL
names(LL)=NULL
#--------------------calculating Va and Vem-------------------------------------
#sigma_a1
#U1TX=crossprod(U1,X)#xiaolei removed, it is re-calculated
#U1TY=crossprod(U1,y)#xiaolei removed, it is re-calculated
sigma_a1=0
for(i in 1:length(d)){
one1=matrix(U1TX[i,], nrow=1)
one2=matrix(U1TY[i,], nrow=1)
sigma_a1_pre=(one2-one1%*%beta)^2/(d[i]+delta)
sigma_a1= sigma_a1+sigma_a1_pre
}
### sigma_a2
#xiaolei removed following 3 lines
#IU=I-tcrossprod(U1,U1) #This needs to be done only once
#IUX=crossprod(IU,X)
#IUY=crossprod(IU,y)
sigma_a2=0
for(i in 1:nrow(U1)){
one1=matrix(IUX[i,], nrow=1)
one2=matrix(IUY[i,], nrow=1)
sigma_a2_pre<-(one2-one1%*%beta)^2
sigma_a2= sigma_a2+sigma_a2_pre
}
sigma_a2<-sigma_a2/delta
sigma_a<- 1/n*(sigma_a1+sigma_a2)
sigma_e<-delta*sigma_a
return(list(beta=beta, delta=delta, LL=LL, vg=sigma_a,ve=sigma_e))
}
)#end of cmpfun(
#=============================================================================================
`GAPIT.kinship.VanRaden` <-
function(snps,hasInbred=TRUE) {
# Object: To calculate the kinship matrix using the method of VanRaden (2009, J. Dairy Sci. 91:4414???C4423)
# Input: snps is n individual rows by m snps columns
# Output: n by n relationship matrix
# Authors: Zhwiu Zhang
# Last update: March 2, 2016
##############################################################################################
print("Calculating kinship with VanRaden method...")
#Remove invariants
fa=colSums(snps)/(2*nrow(snps))
index.non=fa>=1| fa<=0
snps=snps[,!index.non]
nSNP=ncol(snps)
nInd=nrow(snps)
n=nInd
##allele frequency of second allele
p=colSums(snps)/(2*nInd)
P=2*(p-.5) #Difference from .5, multiple by 2
snps=snps-1 #Change from 0/1/2 coding to -1/0/1 coding
print("substracting P...")
Z=t(snps)-P#operation on matrix and vector goes in direction of column
print("Getting X'X...")
#K=tcrossprod((snps), (snps))
K=crossprod((Z), (Z)) #Thanks to Peng Zheng, Meng Huang and Jiafa Chen for finding the problem
print("Adjusting...")
adj=2*sum(p*(1-p))
K=K/adj
print("Calculating kinship with VanRaden method: done")
return(K)
}
#=============================================================================================
`GAPIT.kinship.ZHANG` <-
function(snps,hasInbred=TRUE) {
# Object: To calculate ZHANG (Zones Harbored Adjustments of Negligent Genetic) relationship
# Authors: Zhwiu Zhang
# Last update: october 25, 2014
##############################################################################################
print("Calculating ZHANG relationship defined by Zhiwu Zhang...")
#Remove invariants
fa=colSums(snps)/(2*nrow(snps))
index.non=fa>=1| fa<=0
snps=snps[,!index.non]
het=1-abs(snps-1)
ind.sum=rowSums(het)
fi=ind.sum/(2*ncol(snps))
inbreeding=1-min(fi)
nSNP=ncol(snps)
nInd=nrow(snps)
n=nInd
snpMean= apply(snps,2,mean) #get mean for each snp
print("substracting mean...")
snps=t(snps)-snpMean #operation on matrix and vector goes in direction of column
print("Getting X'X...")
#K=tcrossprod((snps), (snps))
K=crossprod((snps), (snps))
if(is.na(K[1,1])) stop ("GAPIT says: Missing data is not allowed for numerical genotype data")
print("Adjusting...")
#Extract diagonals
i =1:n
j=(i-1)*n
index=i+j
d=K[index]
DL=min(d)
DU=max(d)
floor=min(K)
#Set range between 0 and 2
top=1+inbreeding
K=top*(K-floor)/(DU-floor)
Dmin=top*(DL-floor)/(DU-floor)
#Adjust based on expected minimum diagonal (1)
if(Dmin<1) {
print("Adjustment by the minimum diagonal")
K[index]=(K[index]-Dmin+1)/((top+1-Dmin)*.5)
K[-index]=K[-index]*(1/Dmin)
}
#Limiting the maximum offdiagonal to the top
Omax=max(K[-index])
if(Omax>top){
print("Adjustment by the minimum off diagonal")
K[-index]=K[-index]*(top/Omax)
}
print("Calculating kinship with Zhang method: done")
return(K)
}
#=============================================================================================
`GAPIT.kinship.loiselle` <-
function(snps, method="additive", use="all") {
# Object: To calculate the kinship matrix using the method of Loiselle et al. (1995)
# Authors: Alex Lipka and Hyun Min Kang
# Last update: May 31, 2011
##############################################################################################
#Number of SNP types that are 0s
n0 <- sum(snps==0,na.rm=TRUE)
#Number of heterozygote SNP types
nh <- sum(snps==0.5,na.rm=TRUE)
#Number of SNP types that are 1s
n1 <- sum(snps==1,na.rm=TRUE)
#Number of SNP types that are missing
nNA <- sum(is.na(snps))
#Self explanatory
dim(snps)[1]*dim(snps)[2]
#stopifnot(n0+nh+n1+nNA == length(snps))
#Note that the two lines in if(method == "dominant") and if(method == "recessive") are found in
#if(method == "additive"). Worry about this only if you have heterozygotes, which you do not.
if( method == "dominant" ) {
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) > 0.5),nrow(snps),ncol(snps))
snps[!is.na(snps) && (snps == 0.5)] <- flags[!is.na(snps) && (snps == 0.5)]
}
else if( method == "recessive" ) {
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) < 0.5),nrow(snps),ncol(snps))
snps[!is.na(snps) && (snps == 0.5)] <- flags[!is.na(snps) && (snps == 0.5)]
}
else if( ( method == "additive" ) && ( nh > 0 ) ) {
dsnps <- snps
rsnps <- snps
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) > 0.5),nrow(snps),ncol(snps))
dsnps[!is.na(snps) && (snps==0.5)] <- flags[is.na(snps) && (snps==0.5)]
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) < 0.5),nrow(snps),ncol(snps))
rsnps[!is.na(snps) && (snps==0.5)] <- flags[is.na(snps) && (snps==0.5)]
snps <- rbind(dsnps,rsnps)
}
#mafs is a (# SNPs)x(# lines) matrix. The columns of mafs are identical, and the ij^th element is the average
#allele frequency for the SNP in the i^th row.
#if(use == "all") imputes missing SNP type values with the expected (average) allele frequency.
if( use == "all" ) {
mafs <- matrix(rowMeans(snps,na.rm=TRUE),nrow(snps),ncol(snps))
snps[is.na(snps)] <- mafs[is.na(snps)]
}
else if( use == "complete.obs" ) {
mafs <- matrix(rowMeans(snps,na.rm=TRUE),nrow(snps),ncol(snps))
snps <- snps[rowSums(is.na(snps))==0,]
}
mafs_comp <- 1-mafs
snps_comp <- 1-snps
n <- ncol(snps)
K <- matrix(nrow=n,ncol=n)
diag(K) <- 1
#Create the k term on page 1422 of Loiselle et al. (1995)
missing <- rep(NA, dim(snps)[1])
for(i in 1:dim(snps)[1]) {
missing[i] <- sum(is.na(snps[i,]))
}
for(i in 1:(n-1)) {
for(j in (i+1):n) {
Num_First_Term_1 <- (snps[,i]-mafs[,i])*(snps[,j]-mafs[,j])
Num_First_Term_2 <- (snps_comp[,i]-mafs_comp[,i])*(snps_comp[,j]-mafs_comp[,j])
First_Term <- sum(Num_First_Term_1)+sum(Num_First_Term_2)
Num_Second_Term_1 <- mafs[,i]*(1-mafs[,i])
Num_Second_Term_2 <- mafs_comp[,i]*(1-mafs_comp[,i])
Num_Second_Term_Bias_Correction <- 1/((2*n)-missing - 1)
Num_Second_Term <- Num_Second_Term_1 + Num_Second_Term_2
Second_Term <- sum(Num_Second_Term*Num_Second_Term_Bias_Correction)
Third_Term <- sum(Num_Second_Term)
f <- (First_Term + Second_Term)/Third_Term
K[i,j] <- f
if(K[i,j]<0) K[i,j]=0
K[j,i] <- K[i,j]
}
}
return(K)
}
#=============================================================================================
`GAPIT.kinship.separation` <-
function(PCs=NULL,EV=NULL,nPCs=0 ){
#Object: To calculate kinship from PCS
# PCs: the principal component as columns and individual as rows, the first column is taxa
# EV: Eigen values
# nPCs: the number of front PCs excluded to calculate kinship
#Output: kinship
#Authors: Huihui Li and Zhiwu Zhang
#Last update: April 17, 2012
##############################################################################################
print("Calling GAPIT.kinship.separation")
Total.number.PCs=ncol(PCs)
n=nrow(PCs)
print(Total.number.PCs)
print(n)
#Choose Total.number.PCs-nPCs PCs and EV to calculate K
sep.PCs=PCs[, (nPCs+2):(Total.number.PCs)] #first column is taxa
sep.EV=EV[(nPCs+1):Total.number.PCs]
Weighted.sep.EV=sep.EV/sum(sep.EV)
#X=t(t(sep.PCs)*Weighted.sep.EV)
X=sep.PCs
XMean= apply(X,2,mean)
X=as.matrix(X-XMean)
K=tcrossprod((X), (X))
#Extract diagonals
i =1:n
j=(i-1)*n
index=i+j
d=K[index]
DL=min(d)
DU=max(d)
floor=min(K)
K=(K-floor)/(DL-floor)
MD=(DU-floor)/(DL-floor)
if(is.na(K[1,1])) stop ("GAPIT says: Missing data is not allowed for numerical genotype data")
if(MD>2)K[index]=K[index]/(MD-1)+1
print("GAPIT.kinship.separation called succesfuly")
return (K)
}
#=============================================================================================
if(!require(gplots)) install.packages("gplots")
if(!require(LDheatmap)) install.packages("LDheatmap")
if(!require(genetics)) install.packages("genetics")
if(!require(ape)) install.packages("ape")
if(!require(compiler)) install.packages("compiler")
if(!require(EMMREML)) install.packages("EMMREML")
if(!require(scatterplot3d)) install.packages("scatterplot3d")
if(!'multtest'%in% installed.packages()[,"Package"]){
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("multtest")
BiocManager::install("snpStats")
}
##############################################################################################################################################
###MLMM - Multi-Locus Mixed Model
###SET OF FUNCTIONS TO CARRY GWAS CORRECTING FOR POPULATION STRUCTURE WHILE INCLUDING COFACTORS THROUGH A STEPWISE-REGRESSION APPROACH
#######
#
##note: require EMMA
#library(emma)
#source('emma.r')
#
##REQUIRED DATA & FORMAT
#
#PHENOTYPE - Y: a vector of length m, with names(Y)=individual names
#GENOTYPE - X: a n by m matrix, where n=number of individuals, m=number of SNPs, with rownames(X)=individual names, and colnames(X)=SNP names
#KINSHIP - K: a n by n matrix, with rownames(K)=colnames(K)=individual names
#each of these data being sorted in the same way, according to the individual name
#
##FOR PLOTING THE GWAS RESULTS
#SNP INFORMATION - snp_info: a data frame having at least 3 columns:
# - 1 named 'SNP', with SNP names (same as colnames(X)),
# - 1 named 'Chr', with the chromosome number to which belong each SNP
# - 1 named 'Pos', with the position of the SNP onto the chromosome it belongs to.
#######
#
##FUNCTIONS USE
#save this file somewhere on your computer and source it!
#source('path/mlmm.r')
#
###FORWARD + BACKWARD ANALYSES
#mygwas<-mlmm(Y,X,K,nbchunks,maxsteps)
#X,Y,K as described above
#nbchunks: an integer defining the number of chunks of X to run the analysis, allows to decrease the memory usage ==> minimum=2, increase it if you do not have enough memory
#maxsteps: maximum number of steps desired in the forward approach. The forward approach breaks automatically once the pseudo-heritability is close to 0,
# however to avoid doing too many steps in case the pseudo-heritability does not reach a value close to 0, this parameter is also used.
# It's value must be specified as an integer >= 3
#
###RESULTS
#
##STEPWISE TABLE
#mygwas$step_table
#
##PLOTS
#
##PLOTS FORM THE FORWARD TABLE
#plot_step_table(mygwas,type=c('h2','maxpval','BIC','extBIC'))
#
##RSS PLOT
#plot_step_RSS(mygwas)
#
##GWAS MANHATTAN PLOTS
#
#FORWARD STEPS
#plot_fwd_GWAS(mygwas,step,snp_info,pval_filt)
#step=the step to be plotted in the forward approach, where 1 is the EMMAX scan (no cofactor)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#
#OPTIMAL MODELS
#Automatic identification of the optimal models within the forwrad-backward models according to the extendedBIC or multiple-bonferonni criteria
#
#plot_opt_GWAS(mygwas,opt=c('extBIC','mbonf'),snp_info,pval_filt)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#
##GWAS MANHATTAN PLOT ZOOMED IN A REGION OF INTEREST
#plot_fwd_region(mygwas,step,snp_info,pval_filt,chrom,pos1,pos2)
#step=the step to be plotted in the forward approach, where 1 is the EMMAX scan (no cofactor)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#chrom is an integer specifying the chromosome on which the region of interest is
#pos1, pos2 are integers delimiting the region of interest in the same unit as Pos in snp_info
#
#plot_opt_region(mygwas,opt=c('extBIC','mbonf'),snp_info,pval_filt,chrom,pos1,pos2)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#chrom is an integer specifying the chromosome on which the region of interest is
#pos1, pos2 are integers delimiting the region of interest in the same unit as Pos in snp_info
#
##QQPLOTS of pvalues
#qqplot_fwd_GWAS(mygwas,nsteps)
#nsteps=maximum number of forward steps to be displayed
#
#qqplot_opt_GWAS(mygwas,opt=c('extBIC','mbonf'))
#
##############################################################################################################################################
mlmm<-function(Y,X,K,nbchunks,maxsteps,thresh = NULL) {
n<-length(Y)
m<-ncol(X)
stopifnot(ncol(K) == n)
stopifnot(nrow(K) == n)
stopifnot(nrow(X) == n)
stopifnot(nbchunks >= 2)
stopifnot(maxsteps >= 3)
#INTERCEPT
Xo<-rep(1,n)
#K MATRIX NORMALISATION
K_norm<-(n-1)/sum((diag(n)-matrix(1,n,n)/n)*K)*K
rm(K)
#step 0 : NULL MODEL
cof_fwd<-list()
cof_fwd[[1]]<-as.matrix(Xo)
colnames(cof_fwd[[1]])<-'Xo'
mod_fwd<-list()
mod_fwd[[1]]<-emma.REMLE(Y,cof_fwd[[1]],K_norm)
herit_fwd<-list()
herit_fwd[[1]]<-mod_fwd[[1]]$vg/(mod_fwd[[1]]$vg+mod_fwd[[1]]$ve)
RSSf<-list()
RSSf[[1]]<-'NA'
RSS_H0<-list()
RSS_H0[[1]]<-'NA'
df1<-1
df2<-list()
df2[[1]]<-'NA'
Ftest<-list()
Ftest[[1]]<-'NA'
pval<-list()
pval[[1]]<-'NA'
fwd_lm<-list()
cat('null model done! pseudo-h=',round(herit_fwd[[1]],3),'\n')
#step 1 : EMMAX
M<-solve(chol(mod_fwd[[1]]$vg*K_norm+mod_fwd[[1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cof_fwd[[1]])
fwd_lm[[1]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[1]]$residuals
Q_<-qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[1]])])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[1]])])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[1]])-1))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[2]]<-unlist(RSS)
RSS_H0[[2]]<-sum(Res_H0^2)
df2[[2]]<-n-df1-ncol(cof_fwd[[1]])
Ftest[[2]]<-(rep(RSS_H0[[2]],length(RSSf[[2]]))/RSSf[[2]]-1)*df2[[2]]/df1
pval[[2]]<-pf(Ftest[[2]],df1,df2[[2]],lower.tail=FALSE)
cof_fwd[[2]]<-cbind(cof_fwd[[1]],X[,colnames(X) %in% names(which(RSSf[[2]]==min(RSSf[[2]]))[1])])
colnames(cof_fwd[[2]])<-c(colnames(cof_fwd[[1]]),names(which(RSSf[[2]]==min(RSSf[[2]]))[1]))
mod_fwd[[2]]<-emma.REMLE(Y,cof_fwd[[2]],K_norm)
herit_fwd[[2]]<-mod_fwd[[2]]$vg/(mod_fwd[[2]]$vg+mod_fwd[[2]]$ve)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)
cat('step 1 done! pseudo-h=',round(herit_fwd[[2]],3),'\n')
#FORWARD
for (i in 3:(maxsteps)) {
if (herit_fwd[[i-2]] < 0.01) break else {
M<-solve(chol(mod_fwd[[i-1]]$vg*K_norm+mod_fwd[[i-1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cof_fwd[[i-1]])
fwd_lm[[i-1]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[i-1]]$residuals
Q_ <- qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[i-1]])])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[i-1]])])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[i-1]])-1))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[i]]<-unlist(RSS)
RSS_H0[[i]]<-sum(Res_H0^2)
df2[[i]]<-n-df1-ncol(cof_fwd[[i-1]])
Ftest[[i]]<-(rep(RSS_H0[[i]],length(RSSf[[i]]))/RSSf[[i]]-1)*df2[[i]]/df1
pval[[i]]<-pf(Ftest[[i]],df1,df2[[i]],lower.tail=FALSE)
cof_fwd[[i]]<-cbind(cof_fwd[[i-1]],X[,colnames(X) %in% names(which(RSSf[[i]]==min(RSSf[[i]]))[1])])
colnames(cof_fwd[[i]])<-c(colnames(cof_fwd[[i-1]]),names(which(RSSf[[i]]==min(RSSf[[i]]))[1]))
mod_fwd[[i]]<-emma.REMLE(Y,cof_fwd[[i]],K_norm)
herit_fwd[[i]]<-mod_fwd[[i]]$vg/(mod_fwd[[i]]$vg+mod_fwd[[i]]$ve)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)}
cat('step ',i-1,' done! pseudo-h=',round(herit_fwd[[i]],3),'\n')}
rm(i)
##gls at last forward step
M<-solve(chol(mod_fwd[[length(mod_fwd)]]$vg*K_norm+mod_fwd[[length(mod_fwd)]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cof_fwd[[length(mod_fwd)]])
fwd_lm[[length(mod_fwd)]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[length(mod_fwd)]]$residuals
Q_ <- qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[length(mod_fwd)]])])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[length(mod_fwd)]])])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[length(mod_fwd)]])-1))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[length(mod_fwd)+1]]<-unlist(RSS)
RSS_H0[[length(mod_fwd)+1]]<-sum(Res_H0^2)
df2[[length(mod_fwd)+1]]<-n-df1-ncol(cof_fwd[[length(mod_fwd)]])
Ftest[[length(mod_fwd)+1]]<-(rep(RSS_H0[[length(mod_fwd)+1]],length(RSSf[[length(mod_fwd)+1]]))/RSSf[[length(mod_fwd)+1]]-1)*df2[[length(mod_fwd)+1]]/df1
pval[[length(mod_fwd)+1]]<-pf(Ftest[[length(mod_fwd)+1]],df1,df2[[length(mod_fwd)+1]],lower.tail=FALSE)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)
##get max pval at each forward step
max_pval_fwd<-vector(mode="numeric",length=length(fwd_lm))
max_pval_fwd[1]<-0
for (i in 2:length(fwd_lm)) {max_pval_fwd[i]<-max(fwd_lm[[i]]$coef[2:i,4])}
rm(i)
##get the number of parameters & Loglikelihood from ML at each step
mod_fwd_LL<-list()
mod_fwd_LL[[1]]<-list(nfixed=ncol(cof_fwd[[1]]),LL=emma.MLE(Y,cof_fwd[[1]],K_norm)$ML)
for (i in 2:length(cof_fwd)) {mod_fwd_LL[[i]]<-list(nfixed=ncol(cof_fwd[[i]]),LL=emma.MLE(Y,cof_fwd[[i]],K_norm)$ML)}
rm(i)
cat('backward analysis','\n')
##BACKWARD (1st step == last fwd step)
dropcof_bwd<-list()
cof_bwd<-list()
mod_bwd <- list()
bwd_lm<-list()
herit_bwd<-list()
dropcof_bwd[[1]]<-'NA'
cof_bwd[[1]]<-as.matrix(cof_fwd[[length(mod_fwd)]][,!colnames(cof_fwd[[length(mod_fwd)]]) %in% dropcof_bwd[[1]]])
colnames(cof_bwd[[1]])<-colnames(cof_fwd[[length(mod_fwd)]])[!colnames(cof_fwd[[length(mod_fwd)]]) %in% dropcof_bwd[[1]]]
mod_bwd[[1]]<-emma.REMLE(Y,cof_bwd[[1]],K_norm)
herit_bwd[[1]]<-mod_bwd[[1]]$vg/(mod_bwd[[1]]$vg+mod_bwd[[1]]$ve)
M<-solve(chol(mod_bwd[[1]]$vg*K_norm+mod_bwd[[1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_bwd_t<-crossprod(M,cof_bwd[[1]])
bwd_lm[[1]]<-summary(lm(Y_t~0+cof_bwd_t))
rm(M,Y_t,cof_bwd_t)
for (i in 2:length(mod_fwd)) {
dropcof_bwd[[i]]<-(colnames(cof_bwd[[i-1]])[2:ncol(cof_bwd[[i-1]])])[which(abs(bwd_lm[[i-1]]$coef[2:nrow(bwd_lm[[i-1]]$coef),3])==min(abs(bwd_lm[[i-1]]$coef[2:nrow(bwd_lm[[i-1]]$coef),3])))]
cof_bwd[[i]]<-as.matrix(cof_bwd[[i-1]][,!colnames(cof_bwd[[i-1]]) %in% dropcof_bwd[[i]]])
colnames(cof_bwd[[i]])<-colnames(cof_bwd[[i-1]])[!colnames(cof_bwd[[i-1]]) %in% dropcof_bwd[[i]]]
mod_bwd[[i]]<-emma.REMLE(Y,cof_bwd[[i]],K_norm)
herit_bwd[[i]]<-mod_bwd[[i]]$vg/(mod_bwd[[i]]$vg+mod_bwd[[i]]$ve)
M<-solve(chol(mod_bwd[[i]]$vg*K_norm+mod_bwd[[i]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_bwd_t<-crossprod(M,cof_bwd[[i]])
bwd_lm[[i]]<-summary(lm(Y_t~0+cof_bwd_t))
rm(M,Y_t,cof_bwd_t)}
rm(i)
##get max pval at each backward step
max_pval_bwd<-vector(mode="numeric",length=length(bwd_lm))
for (i in 1:(length(bwd_lm)-1)) {max_pval_bwd[i]<-max(bwd_lm[[i]]$coef[2:(length(bwd_lm)+1-i),4])}
max_pval_bwd[length(bwd_lm)]<-0
##get the number of parameters & Loglikelihood from ML at each step
mod_bwd_LL<-list()
mod_bwd_LL[[1]]<-list(nfixed=ncol(cof_bwd[[1]]),LL=emma.MLE(Y,cof_bwd[[1]],K_norm)$ML)
for (i in 2:length(cof_bwd)) {mod_bwd_LL[[i]]<-list(nfixed=ncol(cof_bwd[[i]]),LL=emma.MLE(Y,cof_bwd[[i]],K_norm)$ML)}
rm(i)
cat('creating output','\n')
##Forward Table: Fwd + Bwd Tables
#Compute parameters for model criteria
BIC<-function(x){-2*x$LL+(x$nfixed+1)*log(n)}
extBIC<-function(x){BIC(x)+2*lchoose(m,x$nfixed-1)}
fwd_table<-data.frame(step=ncol(cof_fwd[[1]])-1,step_=paste('fwd',ncol(cof_fwd[[1]])-1,sep=''),cof='NA',ncof=ncol(cof_fwd[[1]])-1,h2=herit_fwd[[1]]
,maxpval=max_pval_fwd[1],BIC=BIC(mod_fwd_LL[[1]]),extBIC=extBIC(mod_fwd_LL[[1]]))
for (i in 2:(length(mod_fwd))) {fwd_table<-rbind(fwd_table,
data.frame(step=ncol(cof_fwd[[i]])-1,step_=paste('fwd',ncol(cof_fwd[[i]])-1,sep=''),cof=paste('+',colnames(cof_fwd[[i]])[i],sep=''),ncof=ncol(cof_fwd[[i]])-1,h2=herit_fwd[[i]]
,maxpval=max_pval_fwd[i],BIC=BIC(mod_fwd_LL[[i]]),extBIC=extBIC(mod_fwd_LL[[i]])))}
rm(i)
bwd_table<-data.frame(step=length(mod_fwd),step_=paste('bwd',0,sep=''),cof=paste('-',dropcof_bwd[[1]],sep=''),ncof=ncol(cof_bwd[[1]])-1,h2=herit_bwd[[1]]
,maxpval=max_pval_bwd[1],BIC=BIC(mod_bwd_LL[[1]]),extBIC=extBIC(mod_bwd_LL[[1]]))
for (i in 2:(length(mod_bwd))) {bwd_table<-rbind(bwd_table,
data.frame(step=length(mod_fwd)+i-1,step_=paste('bwd',i-1,sep=''),cof=paste('-',dropcof_bwd[[i]],sep=''),ncof=ncol(cof_bwd[[i]])-1,h2=herit_bwd[[i]]
,maxpval=max_pval_bwd[i],BIC=BIC(mod_bwd_LL[[i]]),extBIC=extBIC(mod_bwd_LL[[i]])))}
rm(i,BIC,extBIC,max_pval_fwd,max_pval_bwd,dropcof_bwd)
fwdbwd_table<-rbind(fwd_table,bwd_table)
#RSS for plot
mod_fwd_RSS<-vector()
mod_fwd_RSS[1]<-sum((Y-cof_fwd[[1]]%*%fwd_lm[[1]]$coef[,1])^2)
for (i in 2:length(mod_fwd)) {mod_fwd_RSS[i]<-sum((Y-cof_fwd[[i]]%*%fwd_lm[[i]]$coef[,1])^2)}
mod_bwd_RSS<-vector()
mod_bwd_RSS[1]<-sum((Y-cof_bwd[[1]]%*%bwd_lm[[1]]$coef[,1])^2)
for (i in 2:length(mod_bwd)) {mod_bwd_RSS[i]<-sum((Y-cof_bwd[[i]]%*%bwd_lm[[i]]$coef[,1])^2)}
expl_RSS<-c(1-sapply(mod_fwd_RSS,function(x){x/mod_fwd_RSS[1]}),1-sapply(mod_bwd_RSS,function(x){x/mod_bwd_RSS[length(mod_bwd_RSS)]}))
h2_RSS<-c(unlist(herit_fwd),unlist(herit_bwd))*(1-expl_RSS)
unexpl_RSS<-1-expl_RSS-h2_RSS
plot_RSS<-t(apply(cbind(expl_RSS,h2_RSS,unexpl_RSS),1,cumsum))
#GLS pvals at each step
pval_step<-list()
pval_step[[1]]<-list(out=data.frame("SNP"=colnames(X),"pval"=pval[[2]]),"cof"=NA, "coef"=fwd_lm[[1]]$coef)
for (i in 2:(length(mod_fwd))) {pval_step[[i]]<-list(out=rbind(data.frame(SNP=colnames(cof_fwd[[i]])[-1],'pval'=fwd_lm[[i]]$coef[2:i,4]),
data.frame(SNP=colnames(X)[-which(colnames(X) %in% colnames(cof_fwd[[i]]))],'pval'=pval[[i+1]])),"cof"=colnames(cof_fwd[[i]])[-1], "coef"=fwd_lm[[i]]$coef)}
#GLS pvals for best models according to extBIC and mbonf
opt_extBIC<-fwdbwd_table[which(fwdbwd_table$extBIC==min(fwdbwd_table$extBIC))[1],]
opt_mbonf<-(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),])[which(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),]$ncof==max(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),]$ncof))[1],]
if(! is.null(thresh)){
opt_thresh<-(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),])[which(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),]$ncof==max(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),]$ncof))[1],]
}
bestmodel_pvals<-function(model) {if(substr(model$step_,start=0,stop=3)=='fwd') {
pval_step[[as.integer(substring(model$step_,first=4))+1]]} else if (substr(model$step_,start=0,stop=3)=='bwd') {
cof<-cof_bwd[[as.integer(substring(model$step_,first=4))+1]]
mixedmod<-emma.REMLE(Y,cof,K_norm)
M<-solve(chol(mixedmod$vg*K_norm+mixedmod$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_t<-crossprod(M,cof)
GLS_lm<-summary(lm(Y_t~0+cof_t))
Res_H0<-GLS_lm$residuals
Q_ <- qr.Q(qr(cof_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof)])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof)])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof)-1))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf<-unlist(RSS)
RSS_H0<-sum(Res_H0^2)
df2<-n-df1-ncol(cof)
Ftest<-(rep(RSS_H0,length(RSSf))/RSSf-1)*df2/df1
pval<-pf(Ftest,df1,df2,lower.tail=FALSE)
list('out'=rbind(data.frame(SNP=colnames(cof)[-1],'pval'=GLS_lm$coef[2:(ncol(cof)),4]),
data.frame('SNP'=colnames(X)[-which(colnames(X) %in% colnames(cof))],'pval'=pval)),
'cof'=colnames(cof)[-1],
'coef'=GLS_lm$coef)} else {cat('error \n')}}
opt_extBIC_out<-bestmodel_pvals(opt_extBIC)
opt_mbonf_out<-bestmodel_pvals(opt_mbonf)
if(! is.null(thresh)){
opt_thresh_out<-bestmodel_pvals(opt_thresh)
}
output <- list(step_table=fwdbwd_table,pval_step=pval_step,RSSout=plot_RSS,bonf_thresh=-log10(0.05/m),opt_extBIC=opt_extBIC_out,opt_mbonf=opt_mbonf_out)
if(! is.null(thresh)){
output$thresh <- -log10(thresh)
output$opt_thresh <- opt_thresh_out
}
return(output)
}
##############################################################################################################################################
###MLMM_COF - Multi-Locus Mixed Model
###SET OF FUNCTIONS TO CARRY GWAS CORRECTING FOR POPULATION STRUCTURE WHILE INCLUDING COFACTORS THROUGH A STEPWISE-REGRESSION APPROACH
#######
#
##note: require EMMA
#library(emma)
#source('emma.r')
#
##REQUIRED DATA & FORMAT
#
#PHENOTYPE - Y: a vector of length m, with names(Y)=individual names
#GENOTYPE - X: a n by m matrix, where n=number of individuals, m=number of SNPs, with rownames(X)=individual names, and colnames(X)=SNP names
#KINSHIP - K: a n by n matrix, with rownames(K)=colnames(K)=individual names
#COVARIANCE MATRIX - cofs: a n by p matrix, where n=number of individuals, p=number of covariates in the matrix (e.g. PC axes)
#each of these data being sorted in the same way, according to the individual name
#
##FOR PLOTING THE GWAS RESULTS
#SNP INFORMATION - snp_info: a data frame having at least 3 columns:
# - 1 named 'SNP', with SNP names (same as colnames(X)),
# - 1 named 'Chr', with the chromosome number to which belong each SNP
# - 1 named 'Pos', with the position of the SNP onto the chromosome it belongs to.
#######
#
##FUNCTIONS USE
#save this file somewhere on your computer and source it!
#source('path/mlmm.r')
#
###FORWARD + BACKWARD ANALYSES
#mygwas<-mlmm_cof(Y,X,K,nbchunks,maxsteps)
#X,Y,K as described above
#nbchunks: an integer defining the number of chunks of X to run the analysis, allows to decrease the memory usage ==> minimum=2, increase it if you do not have enough memory
#maxsteps: maximum number of steps desired in the forward approach. The forward approach breaks automatically once the pseudo-heritability is close to 0,
# however to avoid doing too many steps in case the pseudo-heritability does not reach a value close to 0, this parameter is also used.
# It's value must be specified as an integer >= 3
#
###RESULTS
#
##STEPWISE TABLE
#mygwas$step_table
#
##PLOTS
#
##PLOTS FORM THE FORWARD TABLE
#plot_step_table(mygwas,type=c('h2','maxpval','BIC','extBIC'))
#
##RSS PLOT
#plot_step_RSS(mygwas)
#
##GWAS MANHATTAN PLOTS
#
#FORWARD STEPS
#plot_fwd_GWAS(mygwas,step,snp_info,pval_filt)
#step=the step to be plotted in the forward approach, where 1 is the EMMAX scan (no cofactor)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#
#OPTIMAL MODELS
#Automatic identification of the optimal models within the forwrad-backward models according to the extendedBIC or multiple-bonferonni criteria
#
#plot_opt_GWAS(mygwas,opt=c('extBIC','mbonf'),snp_info,pval_filt)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#
##GWAS MANHATTAN PLOT ZOOMED IN A REGION OF INTEREST
#plot_fwd_region(mygwas,step,snp_info,pval_filt,chrom,pos1,pos2)
#step=the step to be plotted in the forward approach, where 1 is the EMMAX scan (no cofactor)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#chrom is an integer specifying the chromosome on which the region of interest is
#pos1, pos2 are integers delimiting the region of interest in the same unit as Pos in snp_info
#
#plot_opt_region(mygwas,opt=c('extBIC','mbonf'),snp_info,pval_filt,chrom,pos1,pos2)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#chrom is an integer specifying the chromosome on which the region of interest is
#pos1, pos2 are integers delimiting the region of interest in the same unit as Pos in snp_info
#
##QQPLOTS of pvalues
#qqplot_fwd_GWAS(mygwas,nsteps)
#nsteps=maximum number of forward steps to be displayed
#
#qqplot_opt_GWAS(mygwas,opt=c('extBIC','mbonf'))
#
##############################################################################################################################################
mlmm_cof<-function(Y,X,cofs,K,nbchunks,maxsteps,thresh = NULL) {
n<-length(Y)
m<-ncol(X)
stopifnot(ncol(K) == n)
stopifnot(nrow(K) == n)
stopifnot(nrow(X) == n)
stopifnot(nrow(cofs) == n)
stopifnot(nbchunks >= 2)
stopifnot(maxsteps >= 3)
#INTERCEPT
Xo<-rep(1,n)
#K MATRIX NORMALISATION
K_norm<-(n-1)/sum((diag(n)-matrix(1,n,n)/n)*K)*K
rm(K)
#step 0 : NULL MODEL
fix_cofs<-cbind(Xo,cofs)
rm(cofs)
addcof_fwd<-list()
addcof_fwd[[1]]<-'NA'
cof_fwd<-list()
cof_fwd[[1]]<-as.matrix(X[,colnames(X) %in% addcof_fwd[[1]]])
mod_fwd<-list()
mod_fwd[[1]]<-emma.REMLE(Y,cbind(fix_cofs,cof_fwd[[1]]),K_norm)
herit_fwd<-list()
herit_fwd[[1]]<-mod_fwd[[1]]$vg/(mod_fwd[[1]]$vg+mod_fwd[[1]]$ve)
RSSf<-list()
RSSf[[1]]<-'NA'
RSS_H0<-list()
RSS_H0[[1]]<-'NA'
df1<-1
df2<-list()
df2[[1]]<-'NA'
Ftest<-list()
Ftest[[1]]<-'NA'
pval<-list()
pval[[1]]<-'NA'
fwd_lm<-list()
cat('null model done! pseudo-h=',round(herit_fwd[[1]],3),'\n')
#step 1 : EMMAX
M<-solve(chol(mod_fwd[[1]]$vg*K_norm+mod_fwd[[1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cbind(fix_cofs,cof_fwd[[1]]))
fwd_lm[[1]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[1]]$residuals
Q_<-qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% addcof_fwd[[1]]])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% addcof_fwd[[1]]])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[1]])))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[2]]<-unlist(RSS)
RSS_H0[[2]]<-sum(Res_H0^2)
df2[[2]]<-n-df1-ncol(fix_cofs)-ncol(cof_fwd[[1]])
Ftest[[2]]<-(rep(RSS_H0[[2]],length(RSSf[[2]]))/RSSf[[2]]-1)*df2[[2]]/df1
pval[[2]]<-pf(Ftest[[2]],df1,df2[[2]],lower.tail=FALSE)
addcof_fwd[[2]]<-names(which(RSSf[[2]]==min(RSSf[[2]]))[1])
cof_fwd[[2]]<-cbind(cof_fwd[[1]],X[,colnames(X) %in% addcof_fwd[[2]]])
colnames(cof_fwd[[2]])[ncol(cof_fwd[[2]])]<-addcof_fwd[[2]]
mod_fwd[[2]]<-emma.REMLE(Y,cbind(fix_cofs,cof_fwd[[2]]),K_norm)
herit_fwd[[2]]<-mod_fwd[[2]]$vg/(mod_fwd[[2]]$vg+mod_fwd[[2]]$ve)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)
cat('step 1 done! pseudo-h=',round(herit_fwd[[2]],3),'\n')
#FORWARD
for (i in 3:(maxsteps)) {
if (herit_fwd[[i-2]] < 0.01) break else {
M<-solve(chol(mod_fwd[[i-1]]$vg*K_norm+mod_fwd[[i-1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cbind(fix_cofs,cof_fwd[[i-1]]))
fwd_lm[[i-1]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[i-1]]$residuals
Q_ <- qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[i-1]])])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[i-1]])])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[i-1]])))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[i]]<-unlist(RSS)
RSS_H0[[i]]<-sum(Res_H0^2)
df2[[i]]<-n-df1-ncol(fix_cofs)-ncol(cof_fwd[[i-1]])
Ftest[[i]]<-(rep(RSS_H0[[i]],length(RSSf[[i]]))/RSSf[[i]]-1)*df2[[i]]/df1
pval[[i]]<-pf(Ftest[[i]],df1,df2[[i]],lower.tail=FALSE)
addcof_fwd[[i]]<-names(which(RSSf[[i]]==min(RSSf[[i]]))[1])
cof_fwd[[i]]<-cbind(cof_fwd[[i-1]],X[,colnames(X) %in% addcof_fwd[[i]]])
colnames(cof_fwd[[i]])[ncol(cof_fwd[[i]])]<-addcof_fwd[[i]]
mod_fwd[[i]]<-emma.REMLE(Y,cbind(fix_cofs,cof_fwd[[i]]),K_norm)
herit_fwd[[i]]<-mod_fwd[[i]]$vg/(mod_fwd[[i]]$vg+mod_fwd[[i]]$ve)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)}
cat('step ',i-1,' done! pseudo-h=',round(herit_fwd[[i]],3),'\n')}
rm(i)
##gls at last forward step
M<-solve(chol(mod_fwd[[length(mod_fwd)]]$vg*K_norm+mod_fwd[[length(mod_fwd)]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cbind(fix_cofs,cof_fwd[[length(mod_fwd)]]))
fwd_lm[[length(mod_fwd)]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[length(mod_fwd)]]$residuals
Q_ <- qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[length(mod_fwd)]])])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[length(mod_fwd)]])])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[length(mod_fwd)]])))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[length(mod_fwd)+1]]<-unlist(RSS)
RSS_H0[[length(mod_fwd)+1]]<-sum(Res_H0^2)
df2[[length(mod_fwd)+1]]<-n-df1-ncol(fix_cofs)-ncol(cof_fwd[[length(mod_fwd)]])
Ftest[[length(mod_fwd)+1]]<-(rep(RSS_H0[[length(mod_fwd)+1]],length(RSSf[[length(mod_fwd)+1]]))/RSSf[[length(mod_fwd)+1]]-1)*df2[[length(mod_fwd)+1]]/df1
pval[[length(mod_fwd)+1]]<-pf(Ftest[[length(mod_fwd)+1]],df1,df2[[length(mod_fwd)+1]],lower.tail=FALSE)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)
##get max pval at each forward step
max_pval_fwd<-vector(mode="numeric",length=length(fwd_lm))
max_pval_fwd[1]<-0
for (i in 2:length(fwd_lm)) {max_pval_fwd[i]<-max(fwd_lm[[i]]$coef[(ncol(fix_cofs)+1):(ncol(fix_cofs)+ncol(cof_fwd[[i]])),4])}
rm(i)
##get the number of parameters & Loglikelihood from ML at each step
mod_fwd_LL<-list()
mod_fwd_LL[[1]]<-list(nfixed=ncol(cbind(fix_cofs,cof_fwd[[1]])),LL=emma.MLE(Y,cbind(fix_cofs,cof_fwd[[1]]),K_norm)$ML)
for (i in 2:length(cof_fwd)) {mod_fwd_LL[[i]]<-list(nfixed=ncol(cbind(fix_cofs,cof_fwd[[i]])),LL=emma.MLE(Y,cbind(fix_cofs,cof_fwd[[i]]),K_norm)$ML)}
rm(i)
cat('backward analysis','\n')
##BACKWARD (1st step == last fwd step)
dropcof_bwd<-list()
cof_bwd<-list()
mod_bwd <- list()
bwd_lm<-list()
herit_bwd<-list()
dropcof_bwd[[1]]<-'NA'
cof_bwd[[1]]<-as.matrix(cof_fwd[[length(mod_fwd)]][,!colnames(cof_fwd[[length(mod_fwd)]]) %in% dropcof_bwd[[1]]])
colnames(cof_bwd[[1]])<-colnames(cof_fwd[[length(mod_fwd)]])[!colnames(cof_fwd[[length(mod_fwd)]]) %in% dropcof_bwd[[1]]]
mod_bwd[[1]]<-emma.REMLE(Y,cbind(fix_cofs,cof_bwd[[1]]),K_norm)
herit_bwd[[1]]<-mod_bwd[[1]]$vg/(mod_bwd[[1]]$vg+mod_bwd[[1]]$ve)
M<-solve(chol(mod_bwd[[1]]$vg*K_norm+mod_bwd[[1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_bwd_t<-crossprod(M,cbind(fix_cofs,cof_bwd[[1]]))
bwd_lm[[1]]<-summary(lm(Y_t~0+cof_bwd_t))
rm(M,Y_t,cof_bwd_t)
for (i in 2:length(mod_fwd)) {
dropcof_bwd[[i]]<-colnames(cof_bwd[[i-1]])[which(abs(bwd_lm[[i-1]]$coef[(ncol(fix_cofs)+1):nrow(bwd_lm[[i-1]]$coef),3])==min(abs(bwd_lm[[i-1]]$coef[(ncol(fix_cofs)+1):nrow(bwd_lm[[i-1]]$coef),3])))]
cof_bwd[[i]]<-as.matrix(cof_bwd[[i-1]][,!colnames(cof_bwd[[i-1]]) %in% dropcof_bwd[[i]]])
colnames(cof_bwd[[i]])<-colnames(cof_bwd[[i-1]])[!colnames(cof_bwd[[i-1]]) %in% dropcof_bwd[[i]]]
mod_bwd[[i]]<-emma.REMLE(Y,cbind(fix_cofs,cof_bwd[[i]]),K_norm)
herit_bwd[[i]]<-mod_bwd[[i]]$vg/(mod_bwd[[i]]$vg+mod_bwd[[i]]$ve)
M<-solve(chol(mod_bwd[[i]]$vg*K_norm+mod_bwd[[i]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_bwd_t<-crossprod(M,cbind(fix_cofs,cof_bwd[[i]]))
bwd_lm[[i]]<-summary(lm(Y_t~0+cof_bwd_t))
rm(M,Y_t,cof_bwd_t)}
rm(i)
##get max pval at each backward step
max_pval_bwd<-vector(mode="numeric",length=length(bwd_lm))
for (i in 1:(length(bwd_lm)-1)) {max_pval_bwd[i]<-max(bwd_lm[[i]]$coef[(ncol(fix_cofs)+1):(ncol(fix_cofs)+ncol(cof_bwd[[i]])),4])}
max_pval_bwd[length(bwd_lm)]<-0
##get the number of parameters & Loglikelihood from ML at each step
mod_bwd_LL<-list()
mod_bwd_LL[[1]]<-list(nfixed=ncol(cbind(fix_cofs,cof_bwd[[1]])),LL=emma.MLE(Y,cbind(fix_cofs,cof_bwd[[1]]),K_norm)$ML)
for (i in 2:length(cof_bwd)) {mod_bwd_LL[[i]]<-list(nfixed=ncol(cbind(fix_cofs,cof_bwd[[i]])),LL=emma.MLE(Y,cbind(fix_cofs,cof_bwd[[i]]),K_norm)$ML)}
rm(i)
cat('creating output','\n')
##Forward Table: Fwd + Bwd Tables
#Compute parameters for model criteria
BIC<-function(x){-2*x$LL+(x$nfixed+1)*log(n)}
extBIC<-function(x){BIC(x)+2*lchoose(m,x$nfixed-1)}
fwd_table<-data.frame(step=ncol(cof_fwd[[1]]),step_=paste('fwd',ncol(cof_fwd[[1]]),sep=''),cof=paste('+',addcof_fwd[[1]],sep=''),ncof=ncol(cof_fwd[[1]]),h2=herit_fwd[[1]]
,maxpval=max_pval_fwd[1],BIC=BIC(mod_fwd_LL[[1]]),extBIC=extBIC(mod_fwd_LL[[1]]))
for (i in 2:(length(mod_fwd))) {fwd_table<-rbind(fwd_table,
data.frame(step=ncol(cof_fwd[[i]]),step_=paste('fwd',ncol(cof_fwd[[i]]),sep=''),cof=paste('+',addcof_fwd[[i]],sep=''),ncof=ncol(cof_fwd[[i]]),h2=herit_fwd[[i]]
,maxpval=max_pval_fwd[i],BIC=BIC(mod_fwd_LL[[i]]),extBIC=extBIC(mod_fwd_LL[[i]])))}
rm(i)
bwd_table<-data.frame(step=length(mod_fwd),step_=paste('bwd',0,sep=''),cof=paste('-',dropcof_bwd[[1]],sep=''),ncof=ncol(cof_bwd[[1]]),h2=herit_bwd[[1]]
,maxpval=max_pval_bwd[1],BIC=BIC(mod_bwd_LL[[1]]),extBIC=extBIC(mod_bwd_LL[[1]]))
for (i in 2:(length(mod_bwd))) {bwd_table<-rbind(bwd_table,
data.frame(step=length(mod_fwd)+i-1,step_=paste('bwd',i-1,sep=''),cof=paste('-',dropcof_bwd[[i]],sep=''),ncof=ncol(cof_bwd[[i]]),h2=herit_bwd[[i]]
,maxpval=max_pval_bwd[i],BIC=BIC(mod_bwd_LL[[i]]),extBIC=extBIC(mod_bwd_LL[[i]])))}
rm(i,BIC,extBIC,max_pval_fwd,max_pval_bwd,dropcof_bwd)
fwdbwd_table<-rbind(fwd_table,bwd_table)
#RSS for plot
#null model only with intercept
null<-emma.REMLE(Y,as.matrix(Xo),K_norm)
M<-solve(chol(null$vg*K_norm+null$ve*diag(n)))
Y_t<-crossprod(M,Y)
Xo_t<-crossprod(M,as.matrix(Xo))
null_lm<-summary(lm(Y_t~0+Xo_t))
rm(null,M,Y_t,Xo_t)
RSS_null<-sum((Y-as.matrix(Xo)%*%null_lm$coef[,1])^2)
mod_fwd_RSS<-vector()
mod_fwd_RSS[1]<-sum((Y-cbind(fix_cofs,cof_fwd[[1]])%*%fwd_lm[[1]]$coef[,1])^2)
for (i in 2:length(mod_fwd)) {mod_fwd_RSS[i]<-sum((Y-cbind(fix_cofs,cof_fwd[[i]])%*%fwd_lm[[i]]$coef[,1])^2)}
mod_bwd_RSS<-vector()
mod_bwd_RSS[1]<-sum((Y-cbind(fix_cofs,cof_bwd[[1]])%*%bwd_lm[[1]]$coef[,1])^2)
for (i in 2:length(mod_bwd)) {mod_bwd_RSS[i]<-sum((Y-cbind(fix_cofs,cof_bwd[[i]])%*%bwd_lm[[i]]$coef[,1])^2)}
expl_RSS<-c(1-sapply(mod_fwd_RSS,function(x){x/RSS_null}),1-sapply(mod_bwd_RSS,function(x){x/RSS_null}))
fix_cofs_RSS<-rep(expl_RSS[1],length(expl_RSS))
cofs_RSS<-expl_RSS-fix_cofs_RSS
h2_RSS<-c(unlist(herit_fwd),unlist(herit_bwd))*(1-expl_RSS)
unexpl_RSS<-1-expl_RSS-h2_RSS
plot_RSS<-t(apply(cbind(fix_cofs_RSS,cofs_RSS,h2_RSS,unexpl_RSS),1,cumsum))
#GLS pvals at each step
pval_step<-list()
pval_step[[1]]<-list(out=data.frame('SNP'=names(pval[[2]]),'pval'=pval[[2]]),cof=addcof_fwd[[1]], "coef"=fwd_lm[[1]]$coef)
for (i in 2:(length(mod_fwd))) {
pval_step[[i]]<-list('out'=rbind(data.frame('SNP'=colnames(cof_fwd[[i]]),'pval'=fwd_lm[[i]]$coef[(ncol(fix_cofs)+1):(ncol(fix_cofs)+ncol(cof_fwd[[i]])),4]),
data.frame('SNP'=names(pval[[i+1]]),'pval'=pval[[i+1]])),
'cof'=colnames(cof_fwd[[i]]),
'coef'=fwd_lm[[i]]$coef)
}
#GLS pvals for best models according to extBIC and mbonf
opt_extBIC<-fwdbwd_table[which(fwdbwd_table$extBIC==min(fwdbwd_table$extBIC))[1],]
opt_mbonf<-(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),])[which(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),]$ncof==max(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),]$ncof))[1],]
if(! is.null(thresh)){
opt_thresh<-(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),])[which(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),]$ncof==max(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),]$ncof))[1],]
}
bestmodel_pvals<-function(model) {if(substr(model$step_,start=0,stop=3)=='fwd') {
pval_step[[as.integer(substring(model$step_,first=4))+1]]} else if (substr(model$step_,start=0,stop=3)=='bwd') {
cof<-cof_bwd[[as.integer(substring(model$step_,first=4))+1]]
mixedmod<-emma.REMLE(Y,cbind(fix_cofs,cof),K_norm)
M<-solve(chol(mixedmod$vg*K_norm+mixedmod$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_t<-crossprod(M,cbind(fix_cofs,cof))
GLS_lm<-summary(lm(Y_t~0+cof_t))
Res_H0<-GLS_lm$residuals
Q_ <- qr.Q(qr(cof_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof)])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof)])[,((j)*round(m/nbchunks)+1):(m-ncol(cof))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf<-unlist(RSS)
RSS_H0<-sum(Res_H0^2)
df2<-n-df1-ncol(fix_cofs)-ncol(cof)
Ftest<-(rep(RSS_H0,length(RSSf))/RSSf-1)*df2/df1
pval<-pf(Ftest,df1,df2,lower.tail=FALSE)
list('out'=rbind(data.frame(SNP=colnames(cof),'pval'=GLS_lm$coef[(ncol(fix_cofs)+1):(ncol(fix_cofs)+ncol(cof)),4]),
data.frame('SNP'=names(pval),'pval'=pval)),
'cof'=colnames(cof),
'coef'=GLS_lm$coef)} else {cat('error \n')}}
opt_extBIC_out<-bestmodel_pvals(opt_extBIC)
opt_mbonf_out<-bestmodel_pvals(opt_mbonf)
if(! is.null(thresh)){
opt_thresh_out<-bestmodel_pvals(opt_thresh)
}
output <- list(step_table=fwdbwd_table,pval_step=pval_step,RSSout=plot_RSS,bonf_thresh=-log10(0.05/m),opt_extBIC=opt_extBIC_out,opt_mbonf=opt_mbonf_out)
if(! is.null(thresh)){
output$thresh <- -log10(thresh)
output$opt_thresh <- opt_thresh_out
}
return(output)
}
`GAPIT.replaceNaN` <-
function(LL) {
#handler of grids with NaN log
#Authors: Zhiwu Zhang
# Last update: may 12, 2011
##############################################################################################
#handler of grids with NaN log
index=(LL=="NaN")
if(length(index)>0) theMin=min(LL[!index])
if(length(index)<1) theMin="NaN"
LL[index]=theMin
return(LL)
}
#=============================================================================================
`GAPIT2` <-
function(Y=NULL,G=NULL,GD=NULL,GM=NULL,KI=NULL,Z=NULL,CV=NULL,CV.Inheritance=NULL,GP=NULL,GK=NULL,
group.from=1000000 ,group.to=1000000,group.by=10,DPP=100000,
kinship.cluster="average", kinship.group='Mean',kinship.algorithm="VanRaden",
bin.from=10000,bin.to=10000,bin.by=10000,inclosure.from=10,inclosure.to=10,inclosure.by=10,
SNP.P3D=TRUE,SNP.effect="Add",SNP.impute="Middle",PCA.total=0, PCA.col=NULL,PCA.3d=FALSE,
SNP.fraction = 1, seed = 123, BINS = 20,SNP.test=TRUE,
SNP.MAF=0,FDR.Rate = 1, SNP.FDR=1,SNP.permutation=FALSE,SNP.CV=NULL,SNP.robust="GLM",
file.from=1, file.to=1, file.total=NULL, file.fragment = 99999,file.path=NULL,
file.G=NULL, file.Ext.G=NULL,file.GD=NULL, file.GM=NULL, file.Ext.GD=NULL,file.Ext.GM=NULL,
ngrid = 100, llim = -10, ulim = 10, esp = 1e-10,
LD.chromosome=NULL,LD.location=NULL,LD.range=NULL,
sangwich.top=NULL,sangwich.bottom=NULL,QC=TRUE,GTindex=NULL,LD=0.1,
NJtree.group=NULL,NJtree.type=c("fan","unrooted"),plot.bin=10^5,
file.output=TRUE,cutOff=0.01, Model.selection = FALSE,output.numerical = FALSE,
output.hapmap = FALSE, Create.indicator = FALSE,
QTN=NULL, QTN.round=1,QTN.limit=0, QTN.update=TRUE, QTN.method="Penalty", Major.allele.zero = FALSE,
method.GLM="fast.lm",method.sub="reward",method.sub.final="reward",method.bin="static",
bin.size=c(1000000),bin.selection=c(10,20,50,100,200,500,1000),
memo="",Prior=NULL,ncpus=1,maxLoop=3,threshold.output=.01,
WS=c(1e0,1e3,1e4,1e5,1e6,1e7),alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),maxOut=100,QTN.position=NULL,CG=NULL,
converge=1,iteration.output=FALSE,acceleration=0,iteration.method="accum",PCA.View.output=TRUE,Geno.View.output=TRUE,
plot.style="Oceanic",SUPER_GD=NULL,SUPER_GS=FALSE){
#Object: To perform GWAS and GPS (Genomic Prediction/Selection)
#Designed by Zhiwu Zhang
#Writen by Alex Lipka, Feng Tian ,You Tang and Zhiwu Zhang
#Last update: Oct 23, 2015 by Jiabo Wang add REML threshold and SUPER GK
##############################################################################################
print("--------------------- Welcome to GAPIT ----------------------------")
echo=TRUE
#GAPIT.Version=GAPIT.0000()
Timmer=GAPIT.Timmer(Infor="GAPIT")
Memory=GAPIT.Memory(Infor="GAPIT")
#Genotype processing and calculation Kin and PC
#First call to genotype to setup genotype data
storage_PCA.total<-PCA.total
#if(PCA.total>0){
#if(PCA.total<=3){PCA.total=4}
#}
#BUS algorithm
#if(kinship.algorithm=="FARM-CPU") return (GAPIT.BUS(Y=Y,GDP=GD,GM=GM,CV=CV,
# method.GLM=method.GLM,method.sub=method.sub,method.sub.final=method.sub.final,method.bin=method.bin,
# bin.size=bin.size,bin.selection=bin.selection,file.output=file.output,
# cutOff=cutOff,DPP=DPP,memo=memo,Prior=Prior,ncpus=ncpus,maxLoop=maxLoop,
# kinship.algorithm=kinship.algorithm,GP=GP,threshold.output=threshold.output,
# WS=WS,alpha=alpha,maxOut=maxOut,QTN.position=QTN.position,converge=converge,
# iteration.output=iteration.output,acceleration=acceleration,iteration.method=iteration.method))
myGenotype<-GAPIT.Genotype(G=G,GD=GD,GM=GM,KI=KI,kinship.algorithm=kinship.algorithm,PCA.total=PCA.total,SNP.fraction=SNP.fraction,SNP.test=SNP.test,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,
file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF=SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,NJtree.group=NJtree.group,NJtree.type=NJtree.type,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,
GP=GP,GK=GK,bin.size=NULL,inclosure.size=NULL, Timmer = Timmer,Memory=Memory,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,GTindex=NULL,file.output=file.output, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero,Geno.View.output=Geno.View.output,PCA.col=PCA.col,PCA.3d=PCA.3d)
Timmer=myGenotype$Timmer
Memory=myGenotype$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype for all")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype for all")
KI=myGenotype$KI
PC=myGenotype$PC
genoFormat=myGenotype$genoFormat
hasGenotype=myGenotype$hasGenotype
byFile=myGenotype$byFile
fullGD=myGenotype$fullGD
GD=myGenotype$GD
GI=myGenotype$GI
GT=myGenotype$GT
G=myGenotype$G
chor_taxa=myGenotype$chor_taxa
#print(dim(GD))
#print(dim(GI))
rownames(GD)=GT
colnames(GD)=GI[,1]
if(output.numerical) write.table(GD, "GAPIT.Genotype.Numerical.txt", quote = FALSE, sep = "\t", row.names = TRUE,col.names = NA)
if(output.hapmap) write.table(myGenotype$G, "GAPIT.Genotype.hmp.txt", quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
#In case of null Y and null GP, return genotype only
if(is.null(Y) & is.null(GP)) return (list(GWAS=NULL,GPS=NULL,Pred=NULL,compression=NULL,kinship.optimum=NULL,kinship=myGenotype$KI,PCA=myGenotype$PC,GD=data.frame(cbind(as.data.frame(GT),as.data.frame(GD))),GI=GI,G=myGenotype$G))
#In case of null Y, return genotype only
if(is.null(Y)) return (list(GWAS=NULL,GPS=NULL,Pred=NULL,compression=NULL,kinship.optimum=NULL,kinship=myGenotype$KI,PCA=myGenotype$PC,GD=data.frame(cbind(as.date.frame(GT),as.data.frame(GD))),Gi=GI,G=myGenotype$G))
rm(myGenotype)
gc()
PCA.total<-storage_PCA.total
print("--------------------Processing traits----------------------------------")
if(!is.null(Y)){
print("Phenotype provided!")
if(ncol(Y)<2) stop ("Phenotype should have taxa name and one trait at least. Please correct phenotype file!")
for (trait in 2: ncol(Y)) {
traitname=colnames(Y)[trait]
###Statistical distributions of phenotype
if(!is.null(Y) & file.output)ViewPhenotype<-GAPIT.Phenotype.View(myY=Y[,c(1,trait)],traitname=traitname,memo=memo)
###Correlation between phenotype and principal components
if(!is.null(Y)&!is.null(PC) & file.output & PCA.total>0 & PCA.View.output){
myPPV<-GAPIT.Phenotype.PCA.View(
PC=PC,
myY=Y[,c(1,trait)]
)
}
#print(SNP.fraction)
#print("!!!!")
#print(GT)
print(paste("Processing trait: ",traitname,sep=""))
if(!is.null(memo)) traitname=paste(memo,".",traitname,sep="")
#print("!!!!")
#print(dim(Z))
#print(dim(KI))
#print(group.from)
#print(group.to)
gapitMain <- GAPIT.Main(Y=Y[,c(1,trait)],G=G,GD=GD,GM=GI,KI=KI,Z=Z,CV=CV,CV.Inheritance=CV.Inheritance,GP=GP,GK=GK,SNP.P3D=SNP.P3D,kinship.algorithm=kinship.algorithm,
bin.from=bin.from,bin.to=bin.to,bin.by=bin.by,inclosure.from=inclosure.from,inclosure.to=inclosure.to,inclosure.by=inclosure.by,
group.from=group.from,group.to=group.to,group.by=group.by,kinship.cluster=kinship.cluster,kinship.group=kinship.group,name.of.trait=traitname,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF= SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,PCA.total=PCA.total,GAPIT.Version=GAPIT.Version,
GT=GT, SNP.fraction = SNP.fraction, seed = seed, BINS = BINS,SNP.test=SNP.test,DPP=DPP, SNP.permutation=SNP.permutation,NJtree.group=NJtree.group,NJtree.type=NJtree.type,plot.bin=plot.bin,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,SNP.CV=SNP.CV,SNP.robust=SNP.robust,
genoFormat=genoFormat,hasGenotype=hasGenotype,byFile=byFile,fullGD=fullGD,PC=PC,GI=GI,Timmer = Timmer, Memory = Memory,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,QC=QC,GTindex=GTindex,LD=LD,file.output=file.output,cutOff=cutOff,
Model.selection = Model.selection, Create.indicator = Create.indicator,
QTN=QTN, QTN.round=QTN.round,QTN.limit=QTN.limit, QTN.update=QTN.update, QTN.method=QTN.method, Major.allele.zero=Major.allele.zero,
QTN.position=QTN.position,plot.style=plot.style,SUPER_GS=SUPER_GS,CG=CG,chor_taxa=chor_taxa)
}# end of loop on trait
if(ncol(Y>2) &file.output)
{
Timmer=gapitMain$Timmer
Memory=gapitMain$Memory
file=paste("GAPIT.", "All",".Timming.csv" ,sep = "")
write.table(Timmer, file, quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
file=paste("GAPIT.", "All",".Memory.Stage.csv" ,sep = "")
write.table(Memory, file, quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}
if(ncol(Y)==2) {
if (!SUPER_GS){
#Evaluate Power vs FDR and type I error
myPower=NULL
if(!is.null(gapitMain$GWAS))myPower=GAPIT.Power(WS=WS, alpha=alpha, maxOut=maxOut,seqQTN=QTN.position,GM=GM,GWAS=gapitMain$GWAS)
h2= as.matrix(as.numeric(as.vector(gapitMain$Compression[,5]))/(as.numeric(as.vector(gapitMain$Compression[,5]))+as.numeric(as.vector(gapitMain$Compression[,6]))),length(gapitMain$Compression[,6]),1)
colnames(h2)=c("Heritability")
print("GAPIT accomplished successfully for single trait. Results are saved. GWAS are returned!")
print("It is OK to see this: 'There were 50 or more warnings (use warnings() to see the first 50)'")
return (list(QTN=gapitMain$QTN,GWAS=gapitMain$GWAS,h2=gapitMain$h2,Pred=gapitMain$Pred,compression=as.data.frame(cbind(gapitMain$Compression,h2)),
kinship.optimum=gapitMain$kinship.optimum,kinship=gapitMain$kinship,PCA=gapitMain$PC,
FDR=myPower$FDR,Power=myPower$Power,Power.Alpha=myPower$Power.Alpha,alpha=myPower$alpha,SUPER_GD=gapitMain$SUPER_GD,P=gapitMain$P,effect.snp=gapitMain$effect.snp,effect.cv=gapitMain$effect.cv))
}else{
h2= as.matrix(as.numeric(as.vector(gapitMain$Compression[,5]))/(as.numeric(as.vector(gapitMain$Compression[,5]))+as.numeric(as.vector(gapitMain$Compression[,6]))),length(gapitMain$Compression[,6]),1)
colnames(h2)=c("Heritability")
print("GAPIT accomplished successfully for single trait. Results are saved. GPS are returned!")
print("It is OK to see this: 'There were 50 or more warnings (use warnings() to see the first 50)'")
return (list(QTN=gapitMain$QTN,GWAS=gapitMain$GWAS,h2=gapitMain$h2,Pred=gapitMain$Pred,compression=as.data.frame(cbind(gapitMain$Compression,h2)),
kinship.optimum=gapitMain$kinship.optimum,kinship=gapitMain$kinship,PCA=gapitMain$PC,
SUPER_GD=gapitMain$SUPER_GD,P=gapitMain$P,effect.snp=gapitMain$effect.snp,effect.cv=gapitMain$effect.cv))
}
}else{
print("GAPIT accomplished successfully for multiple traits. Results are saved")
print("It is OK to see this: 'There were 50 or more warnings (use warnings() to see the first 50)'")
return (list(QTN=NULL,GWAS=NULL,h2=NULL,Pred=NULL,compression=NULL,kinship.optimum=NULL,kinship=gapitMain$KI,PCA=gapitMain$PC,P=gapitMain$P,effect.snp=gapitMain$effect.snp,effect.cv=gapitMain$effect.cv))
}
}# end ofdetecting null Y
} #end of GAPIT function
mtmcgowan/FarmCPU documentation built on Dec. 16, 2019, 12:36 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions `GAPIT.0000` GAPIT.AUC `GAPIT.BIPH` `GAPIT.Block` `GAPIT.Bread` `GAPIT.Burger` `GAPIT.Bus` `GAPIT.CVMergePC` circle.plot Densitplot GAPIT.Circle.Manhatton.Plot `GAPIT.Compress` `GAPIT.Compression.Visualization` `GAPIT.Create.Indicator` `GAPIT.DP` `GAPIT.EMMAxP3D` `GAPIT.FDR.TypeI` `GAPIT.Fragment` `GAPIT.GS` `GAPIT.GS.Visualization` `GAPIT.Genotype` `GAPIT.Genotype.View` `GAPIT.HMP2Num` `GAPIT.HapMap` `GAPIT.IC` `GAPIT.ID` `GAPIT.Imputation` `GAPIT.Interactive.GS` `GAPIT.Interactive.Manhattan` `GAPIT.Judge` `GAPIT.Liner` `GAPIT.Log` `GAPIT.MAF` `GAPIT.Main` `GAPIT.Manhattan` `GAPIT.Memory.Object` `GAPIT.Memory` `GAPIT.Multiple.Manhattan` `GAPIT.Numericalization` `GAPIT.PCA` `GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure` `GAPIT.Phenotype.PCA.View` `GAPIT.Phenotype.Simulation` `GAPIT.Phenotype.View` `GAPIT.Power` `GAPIT.Power.compare` `GAPIT.Power.compare.plink` `GAPIT.Prediction` `GAPIT.Pruning` `GAPIT.QC` `GAPIT.QQ` `GAPIT` `GAPIT.ROC` `GAPIT.RandomModel` `GAPIT.RemoveDuplicate` `GAPIT.Report` `GAPIT.SS` `GAPIT.SUPER.FastMLM` `GAPIT.SUPER.GS` `GAPIT.Specify` `GAPIT.Table` `GAPIT.Timmer` `GAPIT.ZmatrixCompress` `GAPIT.ZmatrixFormation` `GAPIT.cross_validation.compare` emma.kinship emma.eigen.L emma.eigen.L.wo.Z emma.eigen.L.w.Z emma.eigen.R emma.eigen.R.wo.Z emma.eigen.R.w.Z emma.delta.ML.LL.wo.Z emma.delta.ML.LL.w.Z emma.delta.ML.dLL.wo.Z emma.delta.ML.dLL.w.Z emma.delta.REML.LL.wo.Z emma.delta.REML.LL.w.Z emma.delta.REML.dLL.wo.Z emma.delta.REML.dLL.w.Z emma.MLE emma.REMLE emma.ML.LRT emma.REML.t `GAPIT.emma.REMLE` `GAPIT.kinship.VanRaden` `GAPIT.kinship.ZHANG` `GAPIT.kinship.loiselle` `GAPIT.kinship.separation` mlmm mlmm_cof `GAPIT.replaceNaN` `GAPIT2`
`GAPIT.0000` <-
function(){
##############################################################################################
#GAPIT: Genome Association and Prediction Integrated Tool
#Objective 1: State of art methods for high power, accuracy and speed;
#Objective 2: User friendly by design, help documents, and web forum;
#Objective 3: Comprehensive output to interpret data and results;
#Objective 4: Informative tables and high quality figures for reports and publication;
#Methods implimented:
# 1. GLM (Structure or Q method for GWAS, Pritchard et. al. Genetics, 2000)
# 2. MLM (Q+K, Yu et. al. Nature Genetics, 2006)
# 3. gBLUP (Marker based kinship, Zhang et. al. Journal of Animal Science, 2007)
# 4. PCA (Zhao et. al. Plos Genetics, 2007)
# 5. EMMA (Kang et. al. Genetics, 2008)
# 6. CMLM (Zhang et. al. Nature Genetics, 2010)
# 7. EMMAx (Kang et. al. Nature Genetics, 2010)
# 8. P3D (Zhang et. al. Nature Genetics, 2010)
# 9. FaST-LMM (Lippert et. al. Nature Methods, 2011)
# 10. ECMLM (Li et. al. BMC Bioogy, 2014)
# 11. SUPER (Wang et. al. PLoS One, 2014)
#Designed by Zhiwu Zhang
#Authors of paper on Bioinformatics (2012, 28:2397-2399): Alex Lipka, Feng Tian, Qishan Wang, Xiaolei Liu, Meng Li,You Tang and Zhiwu Zhang
#Authors of paper on Plant Genome (2016, Vol 9, No. 2): You Tang, Xiaolei Liu, Jiabo Wang, Meng Li, Qishan Wang, Feng Tian, Zhongbin Su, Yuchun Pan, Di Liu, Alexander E. Lipka, Edward S. Buckler, and Zhiwu Zhang
if(!require(multtest))
{
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("multtest")
#source("http://www.bioconductor.org/biocLite.R")
#biocLite("multtest")
}
if(!require(gplots)) install.packages("gplots")
if(!require(LDheatmap)) install.packages("LDheatmap")
if(!require(genetics)) install.packages("genetics")
if(!require(ape)) install.packages("ape")
if(!require(EMMREML)) install.packages("EMMREML")
if(!require(scatterplot3d)) install.packages("scatterplot3d")
#if(!require(scatterplot3d)) install.packages("scatterplot3d")
# required_pkg = c("MASS", "data.table","biganalytics","ape", "magrittr","bigmemory", "gplots", "compiler", "scatterplot3d", "R.utils", "rrBLUP", "BGLR")
# missing_pkg = required_pkg[!(required_pkg %in% installed.packages()[,"Package"])]
# if(length(missing_pkg)) install.packages(missing_pkg, repos="http://cran.rstudio.com/")
if(!'multtest'%in% installed.packages()[,"Package"]){
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("snpStats")
#source("http://www.bioconductor.org/biocLite.R")
#biocLite("multtest")
#biocLite("snpStats")
}
GAPIT.Version="2018.08.18, GAPIT 3.0"
print(paste("All packages are loaded already ! ","GAPIT.Version is ",GAPIT.Version,sep=""))
return(GAPIT.Version)
}
#=============================================================================================
#Object: To calculate Area Under (ROC) Curve (AUC)
#Straitegy: NA
#Output: P value
#intput: beta-power and alpha-fdr or type I error
#Authors: Zhiwu Zhang
#Last update: December 18, 2015
##############################################################################################
GAPIT.AUC=function(beta=NULL,alpha=NULL){
n=length(beta)
#plot(alpha,beta,type="b")
db=beta[-1]-beta[-n]
da=1-.5*(alpha[-1]+alpha[-n])
ab=da*db
AUC=sum(ab)
return(AUC)
}
#=============================================================================================
#Object: To generate binary phenotype
#Straitegy: NA
#Output: binary phenotype (0 and 1's)
#intput: genetic effect (x), hertiability (h2) and ratio of 1's (r)
#Authors: Zhiwu Zhang
#Last update: March 18, 2016
##############################################################################################
`GAPIT.BIPH` <-
function(x=0,h2=.5,r=.25){
#To assign probability for given standard normal variable x and h2
#Author: Zhiwu Zhang
#Last update: Febuary 27, 2016
p=pnorm(x)
srp=1-p-r
sh=1/(1-sqrt(h2))
adj=(r-.5)*(1-sqrt(h2))
f=1/(1+exp(sh*srp))+adj
return(f)
}
#=============================================================================================
`GAPIT.Block` <-
function(Z,GA,KG){
#Object: To split a group kinship into two blocks containing individuals with and without phenotype
#Output: GAU,KW,KO,KWO
#Authors: Zhiwu Zhang and Alex Lipka
# Last update: April 14, 2011
##############################################################################################
# To separate group kiship into two blocks: with and without phenotype.
# A group goes to with phenotype as loog as it has one phenotyped individual.
#find position in group assignment (GA) for the individual associate with phenotype (specified by Z)
#taxa=unique(intersect(as.matrix(Z[1,-1]),GA[,1]))
taxa.Z=as.matrix(Z[1,-1])
taxa.GA=as.matrix(GA[,1])
position=taxa.GA%in%taxa.Z
#Initial block as 2
GAU=cbind(GA,2)
#Assign block as 1 if the individual has phenotype
GAU[position,3]=1
#Modify the non-phenotyped individuals if they in a group with phenotyped individuals
#To find the groups with phenotyped individuals
#update block assignment for all these groups
#get list of group that should be block 1
#grp.12=as.matrix(unique(GAU[,2]))
#grp.1=as.matrix(unique(GAU[which(GAU[,3]==1),2]))
#grp.2= as.matrix(setdiff(grp.12,grp.1))
grp.12=as.matrix(as.vector(unique(GAU[,2])) ) #unique group
grp.1=as.matrix(as.vector(unique(GAU[which(GAU[,3]==1),2])) ) #unique phenotyped group
grp.2= as.matrix(as.vector(setdiff(grp.12,grp.1))) #unique unphenotyped group
numWithout=length(grp.2)
order.1=1:length(grp.1)
order.2=1:length(grp.2)
if(numWithout >0) grpblock=as.matrix(rbind(cbind(grp.1,1,order.1), cbind(grp.2, 2, order.2)))
if(numWithout==0) grpblock=as.matrix( cbind(grp.1,1,order.1), )
order.block=order(as.matrix(GAU[,3]))
colnames(grpblock)=c("grp","block","ID")
#Indicators: 1-Phenotype, 1.5- unphenotyped but in a group with other phenotyped, 2-rest (Zhiwu, Dec 7,2012)
#GAU0 <- merge(GAU[order.block,-3], grpblock, by.x = "X2", by.y = "grp")
#GAU=GAU0[,c(2,1,3,4)]
#print(head(GAU))
GAU1 <- merge(GAU[order.block,], grpblock, by.x = "X2", by.y = "grp")
#print(GAU1)
GAU1[,4]=(as.numeric(GAU1[,3])+as.numeric(GAU1[,4]))/2
#print(GAU1)
GAU=GAU1[,c(2,1,4,5)]
KW=KG[grp.1,grp.1]
KO=KG[grp.2,grp.2]
KWO=KG[grp.1,grp.2]
#write.table(GAU, "GAU.txt", quote = FALSE, sep = "\t", row.names = TRUE,col.names = TRUE)
#print("GAPIT.Block accomplished successfully!")
return(list(GAU=GAU,KW=KW,KO=KO,KWO=KWO))
}#The function GAPIT.Block ends here
#=============================================================================================
`GAPIT.Bread` <-
function(Y=NULL,CV=NULL,Z=NULL,KI=NULL,GK=NULL,GD=NULL,GM=NULL,
method=NULL,delta=NULL,vg=NULL,ve=NULL,LD=0.01,GTindex=NULL,
file.output=TRUE,opt="extBIC"){
#Object: To calculate p-values of SNPs by using method of GLM, MLM, CMLM, FaST, SUPER and DC
#Straitegy: NA
#Output: GWAS, GPS,REMLs,vg,ve,delta
#intput:
#Y: phenotype with columns of taxa,Y1,Y2...
#CV: covariate variables with columns of taxa, v1,v2...
#GD: same as GK. This is the genotype to screen, the columns are taxa,SNP1,SNP2,...
#GK: Genotype data in numerical format, taxa goes to row and snp go ti columns. the first column is taxa
#GM: Genotype map with columns of snpID,chromosome and position
#method: Options are GLM, MLM, CMLM, FaST, SUPER ,FARM-CPU and DC
#Authors: Zhiwu Zhang
#Last update: November 2, 2011
##############################################################################################
#print("GAPIT.SUPER in progress...")
#Performing first screening with GLM
if(method=="GLM"){
#print("---------------screening by GLM----------------------------------")
#print(GTindex)
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
model=("GLM"),
QC=FALSE,
GTindex=GTindex,
file.output=file.output
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with MLM
if(method=="MLM"){
#print("---------------screening by MLM----------------------------------")
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
group.from=nrow(Y),
group.to=nrow(Y),
QC=FALSE,
GTindex=GTindex,
file.output=file.output
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with Compressed MLM
if(method=="CMLM"){
#print("---------------screening by CMLM----------------------------------")
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
group.from=1,
group.to=nrow(Y),
QC=FALSE,
GTindex=GTindex,
file.output=file.output
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with FaST-LMM
if(method=="FaST" | method=="SUPER"| method=="DC")
{
GWAS=NULL
GPS=NULL
if(!is.null(vg) & !is.null(vg) & is.null(delta)) delta=ve/vg
if(is.null(vg) & is.null(ve))
{
myFaSTREML=GAPIT.get.LL(pheno=matrix(Y[,-1],nrow(Y),1),geno=NULL,snp.pool=as.matrix(GK[,-1]),X0=as.matrix(cbind(matrix(1,nrow(CV),1),CV[,-1])))
#print("Transfer data...")
REMLs=-2*myFaSTREML$LL
delta=myFaSTREML$delta
vg=myFaSTREML$vg
ve=myFaSTREML$ve
#GPS=myFaSTREML$GPS
}
mySUPERFaST=GAPIT.SUPER.FastMLM(ys=matrix(Y[,-1],nrow(Y),1),X0=as.matrix(cbind(matrix(1,nrow(CV),1),CV[,-1])),snp.pool=as.matrix(GK[-1]), xs=as.matrix(GD[GTindex,-1]),vg=vg,delta=delta,LD=LD,method=method)
GWAS=cbind(GM,mySUPERFaST$ps,mySUPERFaST$stats,mySUPERFaST$dfs,mySUPERFaST$effect)
}#End of if(method=="FaST" | method=="SUPER")
#FarmCPU
if(method=="FarmCPU")
{
if(!require(bigmemory)) install.packages("bigmemory")
if(!require(biganalytics)) install.packages("biganalytics")
library(bigmemory) #for FARM-CPU
library(biganalytics) #for FARM-CPU
if(!exists('FarmCPU', mode='function'))source("http://www.zzlab.net/FarmCPU/FarmCPU_functions.txt")#web source code
colnames(GM)[1]="SNP"
myFarmCPU=FarmCPU(
Y=Y,#Phenotype
GD=GD,#Genotype
GM=GM,#Map information
CV=CV[,2:ncol(CV)],
file.output=T
)
xs=t(GD[,-1])
#print(dim(xs))
gene_taxa=colnames(GD)[-1]
ss=apply(xs,1,sum)
ns=nrow(GD)
storage=cbind(.5*ss/ns,1-.5*ss/ns)
maf=as.data.frame(cbind(gene_taxa,apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)))
colnames(maf)=c("SNP","maf")
nobs=ns
#print(dim(myFarmCPU$GWAS))
#print(length(maf))
myFarmCPU$GWAS=merge(myFarmCPU$GWAS[,-5],maf, by.x = "SNP", by.y = "SNP")
GWAS=cbind(myFarmCPU$GWAS,nobs)
GWAS=GWAS[order(GWAS$P.value),]
#colnames(GWAS)=c("SNP","Chromosome","Position","mp","mc","maf","nobs")
GPS=myFarmCPU$Pred
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
#colnames(GPS)[3]=c("Prediction")
}
#MLMM
if(method=="MLMM")
{
print(" GWAS by MLMM method !!")
Y=Y[!is.na(Y[,2]),]
taxa_Y=as.character(Y[,1])
taxa_GD=as.character(GD[,1])
taxa_CV=as.character(CV[,1])
GD=GD[taxa_GD%in%taxa_Y,]
CV=CV[taxa_CV%in%taxa_Y,]
#print(dim(Y))
#print(dim(GD))
#print(dim(CV))
KI= GAPIT.kinship.VanRaden(snps=as.matrix(GD[,-1]))
colnames(KI)=as.character(GD[,1])
if(is.null(CV))
{
mymlmm=mlmm(
Y=Y[,2],#Phenotype
X=as.matrix(GD[,-1]),#Genotype
K=as.matrix(KI),
#cofs=CV[,2:ncol(CV)],
nbchunks = 2, maxsteps = 10, thresh = 1.2 * 10^-5)
}else{
mymlmm=mlmm_cof(
Y=Y[,2],#Phenotype
X=as.matrix(GD[,-1]),#Genotype
K=as.matrix(KI),
cofs=as.matrix(CV[,2:ncol(CV)]),
nbchunks = 2, maxsteps = 10, thresh = 1.2 * 10^-5)
}
if(opt=='extBIC'){
GWAS_result=mymlmm$opt_extBIC$out
}
if(opt=='mbonf'){
GWAS_result=mymlmm$opt_mbonf$out
}
if(opt=='thresh'){
GWAS_result=mymlmm$opt_thresh$out
}
colnames(GWAS_result)=c("SNP","P.value")
xs=t(GD[,-1])
#print(dim(xs))
gene_taxa=colnames(GD)[-1]
colnames(GM)=c("SNP","Chromosome","position")
ss=apply(xs,1,sum)
ns=nrow(GD)
storage=cbind(.5*ss/ns,1-.5*ss/ns)
maf=as.data.frame(cbind(gene_taxa,apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)))
colnames(maf)=c("SNP","maf")
nobs=ns
GWAS_GM=merge(GM,GWAS_result, by.x = "SNP", by.y = "SNP")
mc=matrix(NA,nrow(GWAS_GM),1)
GWAS_GM=cbind(GWAS_GM,mc)
GWAS_GM_maf=merge(GWAS_GM,maf, by.x = "SNP", by.y = "SNP")
GWAS=cbind(GWAS_GM_maf,nobs)
#print(head(GWAS))
GWAS=GWAS[order(GWAS$P.value),]
GPS=NULL
#h2=mymlmm$step_table$h2[length(mymlmm$step_table$h2)]
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
colnames(GWAS)=c("SNP","Chromosome","Position","P.value","effec","maf","nobs")
}
#print("GAPIT.Bread succeed!")
return (list(GWAS=GWAS, GPS=GPS,REMLs=REMLs,vg=vg,ve=ve,delta=delta))
} #end of GAPIT.Bread
#=============================================================================================
`GAPIT.Burger` <-
function(Y=NULL,CV=NULL,GK=NULL){
#Object: To calculate likelihood, variances and ratio
#Straitegy: NA
#Output: P value
#intput:
#Y: phenotype with columns of taxa,Y1,Y2...
#CV: covariate variables with columns of taxa,v1,v2...
#GK: Genotype data in numerical format, taxa goes to row and snp go to columns. the first column is taxa (same as GAPIT.bread)
#Authors: Xiaolei Liu ,Jiabo Wang and Zhiwu Zhang
#Last update: November 2, 2015
##############################################################################################
#print("GAPIT.Burger in progress...")
if(!is.null(CV)){
#CV=as.matrix(CV)#change CV to a matrix when it is a vector xiaolei changed here
#theCV=as.matrix(cbind(matrix(1,nrow(CV),1),CV)) ###########for FarmCPU
theCV=as.matrix(cbind(matrix(1,nrow(CV),1),CV[,-1])) #reseted by Jiabo ,CV frame is wrong,and not rm taxa
#############for GAPIT other method GWAS
}else{
theCV=matrix(1,nrow(Y),1)
}
#handler of single column GK
n=nrow(GK)
m=ncol(GK)
if(m>2){
theGK=as.matrix(GK[,-1])
}else{
theGK=matrix(GK[,-1],n,1)
}
myFaSTREML=GAPIT.get.LL(pheno=matrix(Y[,-1],nrow(Y),1),geno=NULL,snp.pool=theGK,X0=theCV )
REMLs=-2*myFaSTREML$LL
delta=myFaSTREML$delta
vg=myFaSTREML$vg
ve=myFaSTREML$ve
#print("GAPIT.Burger succeed!")
return (list(REMLs=REMLs,vg=vg,ve=ve,delta=delta))
} #end of GAPIT.Burger.Bus
#=============================================================================================
`GAPIT.Bus`<-
function(Y=NULL,CV=NULL,Z=NULL,GT=NULL,KI=NULL,GK=NULL,GD=NULL,GM=NULL,
WS=c(1e0,1e3,1e4,1e5,1e6,1e7),alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),
method=NULL,delta=NULL,vg=NULL,ve=NULL,LD=0.01,GTindex=NULL,
cutOff=0.01,Multi_iter=FASLE,windowsize=5e10,
p.threshold=NA,QTN.threshold=0.01,maf.threshold=0.03,
method.GLM="FarmCPU.LM",method.sub="reward",method.sub.final="reward",method.bin="static",
DPP=1000000,bin.size=c(5e5,5e6,5e7),bin.selection=seq(10,100,10),
file.output=TRUE,opt="extBIC"){
#Object: To license data by method
#Output: Coresponding numerical value
# This function is used to run multiple method, Thanks MLMM FarmCPU Blink to share program and code.
#Authors: Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
GR=NULL
#print(head(CV))
if(method=="GLM"){
#print("---------------screening by GLM----------------------------------")
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
group.from=0,
group.to=0,
QC=FALSE,
GTindex=GTindex,
file.output=F
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with MLM
if(method=="MLM"){
#print("---------------screening by MLM----------------------------------")
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
group.from=nrow(Y),
group.to=nrow(Y),
QC=FALSE,
GTindex=GTindex,
file.output=F
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with Compressed MLM
if(method=="CMLM"){
#print("---------------screening by CMLM----------------------------------")
myGAPIT <- GAPIT(
Y=Y,
CV=CV,
Z=Z,
KI=KI,
GD=GD,
GM=GM,
group.from=1,
group.to=nrow(Y),
QC=FALSE,
GTindex=GTindex,
file.output=F
)
GWAS=myGAPIT$GWAS
GPS=myGAPIT$GPS
REMLs=myGAPIT$REMLs
delta=myGAPIT$ve/myGAPIT$va
vg=myGAPIT$vg
ve=myGAPIT$ve
}
#Performing first screening with FaST-LMM
if(method=="FaST" | method=="SUPER"| method=="DC")
{
GWAS=NULL
GPS=NULL
if(!is.null(vg) & !is.null(vg) & is.null(delta)) delta=ve/vg
if(is.null(vg) & is.null(ve))
{
#print("!!!!!!!!!!!!!!!!")
myFaSTREML=GAPIT.get.LL(pheno=matrix(Y[,-1],nrow(Y),1),geno=NULL,snp.pool=as.matrix(GK[,-1]),X0=as.matrix(cbind(matrix(1,nrow(CV),1),CV[,-1])))
#print(myFaSTREML)
#print("Transfer data...")
REMLs=-2*myFaSTREML$LL
delta=myFaSTREML$delta
vg=myFaSTREML$vg
ve=myFaSTREML$ve
#GPS=myFaSTREML$GPS
}
mySUPERFaST=GAPIT.SUPER.FastMLM(ys=matrix(Y[,-1],nrow(Y),1),X0=as.matrix(cbind(matrix(1,nrow(CV),1),CV[,-1])),snp.pool=as.matrix(GK[-1]), xs=as.matrix(GD[GTindex,-1]),vg=vg,delta=delta,LD=LD,method=method)
GWAS=cbind(GM,mySUPERFaST$ps,mySUPERFaST$stats,mySUPERFaST$dfs,mySUPERFaST$effect)
}#End of if(method=="FaST" | method=="SUPER")
if(method=="FarmCPU")
{
if(!require(bigmemory)) install.packages("bigmemory")
if(!require(biganalytics)) install.packages("biganalytics")
library(bigmemory) #for FARM-CPU
library(biganalytics) #for FARM-CPU
if(!exists('FarmCPU', mode='function'))source("http://www.zzlab.net/FarmCPU/FarmCPU_functions.txt")#web source code
colnames(GM)[1]="SNP"
#print(GTindex)
if(!is.null(CV))
{ farmcpuCV=CV[,2:ncol(CV)]
}else{
farmcpuCV=NULL
}
#print(head(farmcpuCV))
# print(dim(GD))
# print(dim(farmcpuCV))
# print(dim(Y))
myFarmCPU=FarmCPU(
Y=Y,#Phenotype
GD=GD,#Genotype
GM=GM,#Map information
CV=farmcpuCV,
cutOff=cutOff,p.threshold=p.threshold,QTN.threshold=QTN.threshold,
maf.threshold=maf.threshold,method.GLM=method.GLM,method.sub=method.sub,
method.sub.final=method.sub.final,method.bin=method.bin,bin.size=c(5e5,5e6,5e7),bin.selection=seq(10,100,10),
file.output=T
)
GWAS=myFarmCPU$GWAS
xs=t(GD[,-1])
# gene_taxa=colnames(GD)[-1]
ss=apply(xs,1,sum)
ns=nrow(GD)
# storage=cbind(.5*ss/ns,1-.5*ss/ns)
# #maf=as.data.frame(cbind(gene_taxa,apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)))
# colnames(maf)=c("SNP","maf")
nobs=ns
# #GWAS=merge(GWAS[,-5],maf, by.x = "SNP", by.y = "SNP")
# GWAS=merge(GWAS[,-5],maf, by.x = "SNP", by.y = "SNP") #Jiabo modified at 2019.3.25
GWAS=cbind(GWAS,nobs)
maf=apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)
GWAS$maf=maf
#print(head(GWAS))
#print("!!!!!!!!!!!!!")
#print(Multi_iter)
if(Multi_iter)
{
sig=GWAS[GWAS[,4]<(cutOff/(nrow(GWAS))),1:5]
sig=sig[!is.na(sig[,4]),]
#windowsize=500000000
sig_position=as.numeric(as.matrix(sig[,1:3])[,2])*10^10+as.numeric(as.matrix(sig[,1:3])[,3])
sig=sig[order(sig_position),]
sig_position=sig_position[order(sig_position)]
sig_diff=abs(sig_position-c(sig_position[-1],0))
sig_diff_index=sig_diff<windowsize
GWAS0=GWAS
#####################
n=nrow(sig)
print("The number of significant markers is")
print(n)
if(n>0)
{
for(i in 1:n)
{
aim_marker=sig[i,]
#print(aim_marker)
aim_order=as.numeric(rownames(aim_marker))
aim_chro=as.character(aim_marker[,2])
aim_position=as.numeric(as.character(aim_marker[,3]))
position=as.numeric(as.matrix(GM)[,3])
aim_area=GM[,2]==aim_chro&position<(aim_position+windowsize)&position>(aim_position-windowsize)
aim_matrix=as.matrix(table(aim_area))
#print(aim_area)
#print(setequal(aim_area,logical(0)))
if(setequal(aim_area,logical(0))) next
if(aim_matrix[rownames(aim_matrix)=="TRUE",1]<10) next
aim_area[GM[,1]==aim_marker[,1]]=FALSE
secondGD=GD[,c(TRUE,aim_area)]
secondGM=GM[aim_area,]
myGAPIT_Second <- FarmCPU(
Y=Y,
GD=secondGD,
GM=secondGM,
CV=farmcpuCV,
file.output=T
)
Second_GWAS= myGAPIT_Second$GWAS [,1:4]
Second_GWAS[is.na(Second_GWAS[,4]),4]=1
orignal_GWAS=GWAS[aim_area,]
GWAS_index=match(Second_GWAS[,1],GWAS[,1])
#test_GWAS=GWAS
GWAS[GWAS_index,4]=Second_GWAS[,4]
}
}
}
#GWAS=GWAS[order(GWAS$P.value),]
#colnames(GWAS)=c("SNP","Chromosome","Position","mp","mc","maf","nobs")
#print(head(GWAS))
GWAS[,2]=as.numeric(as.character(GWAS[,2]))
GWAS[,3]=as.numeric(as.character(GWAS[,3]))
#rint(head(GWAS))
nobs=ns
# #GWAS=merge(GWAS[,-5],maf, by.x = "SNP", by.y = "SNP")
# GWAS=merge(GWAS[,-5],maf, by.x = "SNP", by.y = "SNP") #Jiabo modified at 2019.3.25
#GWAS=cbind(GWAS,nobs)
#print(head(GWAS))
GWAS=GWAS[,c(1:5,7,6)]
GR=GAPIT.RandomModel(Y=Y,X=GD[,-1],GWAS=GWAS,CV=cbind(Y[,1],farmcpuCV),cutOff=cutOff,GT=GT)
GPS=myFarmCPU$Pred
#colnames(GPS)[3]=c("Prediction")
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
#print(dim(GWAS))
#print(head(GWAS))
print("FarmCPU has been done succeedly!!")
}
if(method=="BlinkC")
{
blink_GD=t(GD[,-1])
blink_GM=GM
blink_Y=Y
blink_Y[is.na(blink_Y)]="NaN"
colnames(blink_Y)=c("taxa","trait1")
blink_CV=CV
write.table(blink_GD,"myData.dat",quote=F,col.names=F,row.names=F)
write.table(blink_GM,"myData.map",quote=F,col.names=T,row.names=F)
write.table(blink_Y,"myData.txt",quote=F,col.names=T,row.names=F)
if(!is.null(CV))
{
write.table(blink_CV,"myData.cov",quote=F,col.names=T,row.names=F)
}else{
system("rm myData.cov")
}
system("./blink --gwas --file myData --numeric")
result=read.table("trait1_GWAS_result.txt",head=T)
result=result[,c(1,2,3,5,4)]
xs=t(GD[,-1])
#print(dim(xs))
gene_taxa=colnames(GD)[-1]
ss=apply(xs,1,sum)
ns=nrow(GD)
storage=cbind(.5*ss/ns,1-.5*ss/ns)
maf=result[,5]
#colnames(maf)=c("SNP","maf")
nobs=ns
effect=rep(NA,length(nobs))
#myFarmCPU$GWAS=merge(myFarmCPU$GWAS[,-5],maf, by.x = "SNP", by.y = "SNP")
GWAS=cbind(result[,1:4],effect)
GWAS=cbind(GWAS,maf)
GWAS=cbind(GWAS,nobs)
GWAS[,2]=as.numeric(as.character(GWAS[,2]))
GWAS[,3]=as.numeric(as.character(GWAS[,3]))
#print(dim(GWAS))
#GWAS=GWAS[order(GWAS$P.value),]
colnames(GWAS)=c("SNP","Chromosome","Position","P.value","effec","maf","nobs")
GPS=NULL
#colnames(GPS)[3]=c("Prediction")
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
}
if(method=="Blink")
{
if(!require(devtools)) install.packages("devtools")
if(!require(BLINK)) devtools::install_github("YaoZhou89/BLINK")
#source("http://zzlab.net/GAPIT/gapit_functions.txt")
source("http://zzlab.net/FarmCPU/FarmCPU_functions.txt")
blink_GD=t(GD[,-1])
blink_GM=GM
blink_Y=Y
blink_CV=NULL
if(!is.null(CV))blink_CV=CV[,-1]
#print(head(blink_CV))
library(BLINK)
myBlink=Blink(Y=blink_Y,GD=blink_GD,GM=blink_GM,CV=blink_CV,maxLoop=10,time.cal=T)
#print(head(myBlink$GWAS))
GWAS=myBlink$GWAS[,1:4]
#print(str(myBlink))
ns=nrow(GD)
nobs=ns
effect=rep(NA,length(nobs))
xs=t(GD[,-1])
ss=apply(xs,1,sum)
#storage=cbind(.5*ss/ns,1-.5*ss/ns)
maf=apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)
GWAS=cbind(GWAS,maf)#, by.x = "SNP", by.y = "SNP") #Jiabo modified at 2019.3.25
GWAS=cbind(GWAS,effect)
GWAS=cbind(GWAS,nobs)
# gene_taxa=as.character(blink_GM[,1])
# ss=apply(blink_GD,1,sum)
# ns=nrow(GD)
# nobs=ns
# storage=cbind(.5*ss/ns,1-.5*ss/ns)
# maf=as.data.frame(cbind(gene_taxa,apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)))
# colnames(maf)=c("SNP","maf")
# effect=rep(NA,length(nobs))
# GWAS=cbind(GWAS,effect)
# GWAS=cbind(GWAS,maf)
# GWAS=cbind(GWAS,nobs)
# GWAS[,2]=as.numeric(as.character(GWAS[,2]))
# GWAS[,3]=as.numeric(as.character(GWAS[,3]))
# GPS=myBlink$Pred
#colnames(GPS)[3]=c("Prediction")
if(Multi_iter)
{
sig=GWAS[GWAS[,4]<(cutOff/(nrow(GWAS))),1:5]
sig=sig[!is.na(sig[,4]),]
#windowsize=500000000
sig_position=as.numeric(as.matrix(sig[,1:3])[,2])*10^10+as.numeric(as.matrix(sig[,1:3])[,3])
sig=sig[order(sig_position),]
sig_position=sig_position[order(sig_position)]
sig_diff=abs(sig_position-c(sig_position[-1],0))
sig_diff_index=sig_diff<windowsize
GWAS0=GWAS
#####################
n=nrow(sig)
print("The number of significant markers is")
print(n)
if(n>0)
{
for(i in 1:n)
{
aim_marker=sig[i,]
#print(aim_marker)
aim_order=as.numeric(rownames(aim_marker))
aim_chro=as.character(aim_marker[,2])
aim_position=as.numeric(as.character(aim_marker[,3]))
position=as.numeric(as.matrix(GM)[,3])
aim_area=GM[,2]==aim_chro&position<(aim_position+windowsize)&position>(aim_position-windowsize)
aim_matrix=as.matrix(table(aim_area))
if(setequal(aim_area,logical(0))) next
if(aim_matrix[rownames(aim_matrix)=="TRUE",1]<10) next
aim_area[GM[,1]==aim_marker[,1]]=FALSE
secondGD=GD[,c(TRUE,aim_area)]
secondGM=GM[aim_area,]
myGAPIT_Second =Blink(Y=Y,GD=secondGD,GM=secondGM,CV=blink_CV,maxLoop=10,time.cal=T)
#print(head(myBlink$GWAS))
#GWAS=myBlink$GWAS[,1:4]
Second_GWAS= myGAPIT_Second$GWAS [,1:4]
Second_GWAS[is.na(Second_GWAS[,4]),4]=1
orignal_GWAS=GWAS[aim_area,]
GWAS_index=match(Second_GWAS[,1],GWAS[,1])
#test_GWAS=GWAS
GWAS[GWAS_index,4]=Second_GWAS[,4]
}
}
}
#GWAS=GWAS[order(GWAS$P.value),]
#colnames(GWAS)=c("SNP","Chromosome","Position","mp","mc","maf","nobs")
#print(head(GWAS))
GWAS[,2]=as.numeric(as.character(GWAS[,2]))
GWAS[,3]=as.numeric(as.character(GWAS[,3]))
#rint(head(GWAS))
GPS=myBlink$Pred
#colnames(GPS)[3]=c("Prediction")
#print(head(GWAS))
GWAS=GWAS[,c(1:5,7,6)]
GR=GAPIT.RandomModel(Y=blink_Y,X=GD[,-1],GWAS=GWAS,CV=CV,cutOff=cutOff,GT=GT)
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
#print(dim(GWAS))
#print(head(GWAS))
print("Bink R is done !!!!!")
}
if(method=="MLMM")
{
print("GWAS by MLMM method !!")
Y=Y[!is.na(Y[,2]),]
taxa_Y=as.character(Y[,1])
taxa_GD=as.character(GD[,1])
taxa_CV=as.character(CV[,1])
GD=GD[taxa_GD%in%taxa_Y,]
CV=CV[taxa_CV%in%taxa_Y,]
#print(dim(Y))
#print(dim(GD))
if(is.null(KI))
{
KI= GAPIT.kinship.VanRaden(snps=as.matrix(GD[,-1]))
colnames(KI)=as.character(GD[,1])
}else{
print("The Kinship is provided by user !!")
KI=KI[,-1]
#colnames(KI)=as.character(GD[,1])
taxa_KI=as.character(colnames(KI))
KI=KI[taxa_KI%in%as.character(GD[,1]),taxa_KI%in%as.character(GD[,1])]
}
if(ncol(KI)!=nrow(GD)) print("Please make sure dim of K equal number of GD !!")
# print(dim(KI))
# print(dim(GD))
# print(KI[1:5,1:5])
if(is.null(CV))
{
mymlmm=mlmm(
Y=Y[,2],#Phenotype
X=as.matrix(GD[,-1]),#Genotype
K=as.matrix(KI),
#cofs=CV[,2:ncol(CV)],
nbchunks = 2, maxsteps = 10, thresh = 1.2 * 10^-5)
}else{
mymlmm=mlmm_cof(
Y=Y[,2],#Phenotype
X=as.matrix(GD[,-1]),#Genotype
K=as.matrix(KI),
cofs=as.matrix(CV[,2:ncol(CV)]),
nbchunks = 2, maxsteps = 10, thresh = 1.2 * 10^-5)
}
if(opt=='extBIC'){
GWAS_result=mymlmm$opt_extBIC$out
}
if(opt=='mbonf'){
GWAS_result=mymlmm$opt_mbonf$out
}
if(opt=='thresh'){
GWAS_result=mymlmm$opt_thresh$out
}
colnames(GWAS_result)=c("SNP","P.value")
xs=t(GD[,-1])
#print(dim(xs))
gene_taxa=colnames(GD)[-1]
colnames(GM)=c("SNP","Chromosome","position")
ss=apply(xs,1,sum)
ns=nrow(GD)
storage=cbind(.5*ss/ns,1-.5*ss/ns)
maf=as.data.frame(cbind(gene_taxa,apply(cbind(.5*ss/ns,1-.5*ss/ns),1,min)))
colnames(maf)=c("SNP","maf")
nobs=ns
GWAS_GM=merge(GM,GWAS_result, by.x = "SNP", by.y = "SNP")
mc=matrix(NA,nrow(GWAS_GM),1)
GWAS_GM=cbind(GWAS_GM,mc)
#print(head(GWAS_GM))
#print(head(maf))
#maf=NULL
GWAS_GM_maf=merge(GWAS_GM,maf, by.x = "SNP", by.y = "SNP")
GWAS=cbind(GWAS_GM_maf,nobs)
#print(head(GWAS))
GWAS=GWAS[order(GWAS$P.value),]
GWAS[,2]=as.numeric(as.character(GWAS[,2]))
GWAS[,3]=as.numeric(as.character(GWAS[,3]))
GPS=NULL
#h2=mymlmm$step_table$h2[length(mymlmm$step_table$h2)]
h2=NULL
vg=NULL
ve=NULL
delta=NULL
REMLs=NULL
colnames(GWAS)=c("SNP","Chromosome","Position","P.value","effect","maf","nobs")
}
#print("GAPIT.Bus succeed!")
return (list(GWAS=GWAS, GPS=GPS,REMLs=REMLs,vg=vg,ve=ve,delta=delta,GVs=GR$GVs))
} #end of GAPIT.Bus
#=============================================================================================
`GAPIT.CVMergePC` <-
function(X,Y){
#Object: To convert character SNP genotpe to numerical
#Output: Coresponding numerical value
#Authors: Feng Tian and Zhiwu Zhang
# Last update: May 30, 2011
##############################################################################################
#Z=X+Y
Z <- merge(X, Y, by.x = colnames(X)[1], by.y = colnames(Y)[1])
return(Z)
}#end of GAPIT.CVMergePCfunction
#=============================================================================================
########## These three functions come from MVP package, Jiabo did some modifications
########## Following Apache License, we thank MVP developper to build these functions.
########## 1 creat P value scale in addtitional chromsome
########## 2 set col is same as GAPIT
########## 3
circle.plot <- function(myr,type="l",x=NULL,lty=1,lwd=1,col="black",add=TRUE,n.point=1000)
{
curve(sqrt(myr^2-x^2),xlim=c(-myr,myr),n=n.point,ylim=c(-myr,myr),type=type,lty=lty,col=col,lwd=lwd,add=add)
curve(-sqrt(myr^2-x^2),xlim=c(-myr,myr),n=n.point,ylim=c(-myr,myr),type=type,lty=lty,col=col,lwd=lwd,add=TRUE)
}
Densitplot <- function(
map,
col=c("darkblue", "white", "red"),
main="SNP Density",
bin=1e6,
band=3,
width=5,
legend.len=10,
legend.max=NULL,
legend.pt.cex=3,
legend.cex=1,
legend.y.intersp=1,
legend.x.intersp=1,
plot=TRUE
)
{ #print(head(map))
map <- as.matrix(map)
map <- map[!is.na(map[, 2]), ]
map <- map[!is.na(map[, 3]), ]
map <- map[map[, 2] != 0, ]
#map <- map[map[, 3] != 0, ]
options(warn = -1)
max.chr <- max(as.numeric(map[, 2]), na.rm=TRUE)
if(is.infinite(max.chr)) max.chr <- 0
map.xy.index <- which(!as.numeric(map[, 2]) %in% c(0 : max.chr))
if(length(map.xy.index) != 0){
chr.xy <- unique(map[map.xy.index, 2])
for(i in 1:length(chr.xy)){
map[map[, 2] == chr.xy[i], 2] <- max.chr + i
}
}
map <- map[order(as.numeric(map[, 2]), as.numeric(map[, 3])), ]
chr <- as.numeric(map[, 2])
pos <- as.numeric(map[, 3])
chr.num <- unique(chr)
#print(chr.num)
chorm.maxlen <- max(pos)
if(plot) plot(NULL, xlim=c(0, chorm.maxlen + chorm.maxlen/10), ylim=c(0, length(chr.num) * band + band), main=main,axes=FALSE, xlab="", ylab="", xaxs="i", yaxs="i")
pos.x <- list()
col.index <- list()
maxbin.num <- NULL
#print(chr.num)
for(i in 1 : length(chr.num)){
pos.x[[i]] <- pos[which(chr == chr.num[i])]
cut.len <- ceiling((max(pos.x[[i]]) - min(pos.x[[i]])) / bin)
if(cut.len <= 1){
col.index[[i]] = 1
}else{
cut.r <- cut(pos.x[[i]], cut.len, labels=FALSE)
eachbin.num <- table(cut.r)
#print(eachbin.num)
maxbin.num <- c(maxbin.num, max(eachbin.num))
col.index[[i]] <- rep(eachbin.num, eachbin.num)
}
}
Maxbin.num <- max(maxbin.num)
maxbin.num <- Maxbin.num
if(!is.null(legend.max)){
maxbin.num <- legend.max
}
#print(col)
#print(maxbin.num)
col=colorRampPalette(col)(maxbin.num)
col.seg=NULL
for(i in 1 : length(chr.num)){
if(plot) polygon(c(0, 0, max(pos.x[[i]]), max(pos.x[[i]])),
c(-width/5 - band * (i - length(chr.num) - 1), width/5 - band * (i - length(chr.num) - 1),
width/5 - band * (i - length(chr.num) - 1), -width/5 - band * (i - length(chr.num) - 1)), col="grey", border="grey")
if(!is.null(legend.max)){
if(legend.max < Maxbin.num){
col.index[[i]][col.index[[i]] > legend.max] <- legend.max
}
}
col.seg <- c(col.seg, col[round(col.index[[i]] * length(col) / maxbin.num)])
if(plot) segments(pos.x[[i]], -width/5 - band * (i - length(chr.num) - 1), pos.x[[i]], width/5 - band * (i - length(chr.num) - 1),
col=col[round(col.index[[i]] * length(col) / maxbin.num)], lwd=1)
}
if(length(map.xy.index) != 0){
for(i in 1:length(chr.xy)){
chr.num[chr.num == max.chr + i] <- chr.xy[i]
}
}
chr.num <- rev(chr.num)
if(plot) mtext(at=seq(band, length(chr.num) * band, band),text=paste("Chr", chr.num, sep=""), side=2, las=2, font=1, cex=0.6, line=0.2)
if(plot) axis(3, at=seq(0, chorm.maxlen, length=10), labels=c(NA, paste(round((seq(0, chorm.maxlen, length=10))[-1] / 1e6, 0), "Mb", sep="")),
font=1, cex.axis=0.8, tck=0.01, lwd=2, padj=1.2)
# image(c(chorm.maxlen-chorm.maxlen * legend.width / 20 , chorm.maxlen),
# round(seq(band - width/5, (length(chr.num) * band + band) * legend.height / 2 , length=maxbin.num+1), 2),
# t(matrix(0 : maxbin.num)), col=c("white", rev(heat.colors(maxbin.num))), add=TRUE)
legend.y <- round(seq(0, maxbin.num, length=legend.len))
len <- legend.y[2]
legend.y <- seq(0, maxbin.num, len)
if(!is.null(legend.max)){
if(legend.max < Maxbin.num){
if(!maxbin.num %in% legend.y){
legend.y <- c(legend.y, paste(">=", maxbin.num, sep=""))
legend.y.col <- c(legend.y[c(-1, -length(legend.y))], maxbin.num)
}else{
legend.y[length(legend.y)] <- paste(">=", maxbin.num, sep="")
legend.y.col <- c(legend.y[c(-1, -length(legend.y))], maxbin.num)
}
}else{
if(!maxbin.num %in% legend.y){
legend.y <- c(legend.y, maxbin.num)
}
legend.y.col <- c(legend.y[-1])
}
}else{
if(!maxbin.num %in% legend.y){
legend.y <- c(legend.y, paste(">", max(legend.y), sep=""))
legend.y.col <- c(legend.y[c(-1, -length(legend.y))], maxbin.num)
}else{
legend.y.col <- c(legend.y[-1])
}
}
legend.y.col <- as.numeric(legend.y.col)
legend.col <- c("grey", col[round(legend.y.col * length(col) / maxbin.num)])
if(plot) legend(x=(chorm.maxlen + chorm.maxlen/100), y=( -width/2.5 - band * (length(chr.num) - length(chr.num) - 1)), title="", legend=legend.y, pch=15, pt.cex = legend.pt.cex, col=legend.col,
cex=legend.cex, bty="n", y.intersp=legend.y.intersp, x.intersp=legend.x.intersp, yjust=0, xjust=0, xpd=TRUE)
if(!plot) return(list(den.col=col.seg, legend.col=legend.col, legend.y=legend.y))
}
GAPIT.Circle.Manhatton.Plot <- function(
Pmap,
col=c("#377EB8", "#4DAF4A", "#984EA3", "#FF7F00"),
#col=c("darkgreen", "darkblue", "darkyellow", "darkred"),
bin.size=1e6,
bin.max=NULL,
pch=19,
band=1,
cir.band=0.5,
H=1.5,
ylim=NULL,
cex.axis=1,
plot.type="c",
multracks=TRUE,
cex=c(0.5,0.8,1),
r=0.3,
xlab="Chromosome",
ylab=expression(-log[10](italic(p))),
xaxs="i",
yaxs="r",
outward=TRUE,
threshold = 0.01,
threshold.col="red",
threshold.lwd=1,
threshold.lty=2,
amplify= TRUE, # is that available for remark signal pch col
chr.labels=NULL,
signal.cex = 2,
signal.pch = 8,
signal.col="red",
signal.line=NULL,
cir.chr=TRUE,
cir.chr.h=1.3,
chr.den.col=c("darkgreen", "yellow", "red"),
#chr.den.col=c(126,177,153),
cir.legend=TRUE,
cir.legend.cex=0.8,
cir.legend.col="grey45",
LOG10=TRUE,
box=FALSE,
conf.int.col="grey",
file.output=TRUE,
file="pdf",
dpi=300,
xz=NULL,
memo=""
)
{ #print("Starting Circular-Manhattan plot!",quote=F)
taxa=colnames(Pmap)[-c(1:3)]
if(!is.null(memo) && memo != "") memo <- paste("_", memo, sep="")
if(length(taxa) == 0) taxa <- "Index"
taxa <- paste(taxa, memo, sep="")
col=rep(c( '#FF6A6A', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(length(taxa)/5))
legend.bit=round(nrow(Pmap)/30)
numeric.chr <- as.numeric(Pmap[, 1])
options(warn = 0)
max.chr <- max(numeric.chr, na.rm=TRUE)
aa=Pmap[1:legend.bit,]
aa[,2]=max.chr+1
#print(aa[,3])
aa[,3]=sample(1:10^7.5,legend.bit)
aa[,-c(1:3)]=0
Pmap=rbind(Pmap,aa)
#print(unique(Pmap[,2]))
#SNP-Density plot
if("d" %in% plot.type){
print("SNP_Density Plotting...")
if(file.output){
if(file=="jpg") jpeg(paste("SNP_Density.",paste(taxa,collapse="."),".jpg",sep=""), width = 9*dpi,height=7*dpi,res=dpi,quality = 100)
if(file=="pdf") pdf(paste("GAPIT.", taxa,".SNP_Density.Plot.pdf" ,sep=""), width = 9,height=7)
if(file=="tiff") tiff(paste("SNP_Density.",paste(taxa,collapse="."),".tiff",sep=""), width = 9*dpi,height=7*dpi,res=dpi)
par(xpd=TRUE)
}else{
if(is.null(dev.list())) dev.new(width = 9,height=7)
par(xpd=TRUE)
}
Densitplot(map=Pmap[,c(1:3)], col=col, bin=bin.size, legend.max=bin.max, main=paste("The number of SNPs within ", bin.size/1e6, "Mb window size", sep=""))
if(file.output) dev.off()
}
if(length(plot.type) !=1 | (!"d" %in% plot.type)){
#order Pmap by the name of SNP
#Pmap=Pmap[order(Pmap[,1]),]
Pmap <- as.matrix(Pmap)
#delete the column of SNPs names
Pmap <- Pmap[,-1]
Pmap[is.na(Pmap)]=1
#print(dim(Pmap))
#scale and adjust the parameters
cir.chr.h <- cir.chr.h/5
cir.band <- cir.band/5
threshold=threshold/nrow(Pmap)
if(!is.null(threshold)){
threshold.col <- rep(threshold.col,length(threshold))
threshold.lwd <- rep(threshold.lwd,length(threshold))
threshold.lty <- rep(threshold.lty,length(threshold))
signal.col <- rep(signal.col,length(threshold))
signal.pch <- rep(signal.pch,length(threshold))
signal.cex <- rep(signal.cex,length(threshold))
}
if(length(cex)!=3) cex <- rep(cex,3)
if(!is.null(ylim)){
if(length(ylim)==1) ylim <- c(0,ylim)
}
if(is.null(conf.int.col)) conf.int.col <- NA
if(is.na(conf.int.col)){
conf.int=FALSE
}else{
conf.int=TRUE
}
#get the number of traits
R=ncol(Pmap)-2
#replace the non-euchromosome
options(warn = -1)
numeric.chr <- as.numeric(Pmap[, 1])
options(warn = 0)
max.chr <- max(numeric.chr, na.rm=TRUE)
if(is.infinite(max.chr)) max.chr <- 0
map.xy.index <- which(!numeric.chr %in% c(0:max.chr))
if(length(map.xy.index) != 0){
chr.xy <- unique(Pmap[map.xy.index, 1])
for(i in 1:length(chr.xy)){
Pmap[Pmap[, 1] == chr.xy[i], 1] <- max.chr + i
}
}
Pmap <- matrix(as.numeric(Pmap), nrow(Pmap))
#order the GWAS results by chromosome and position
Pmap <- Pmap[order(Pmap[, 1], Pmap[,2]), ]
#get the index of chromosome
chr <- unique(Pmap[,1])
chr.ori <- chr
if(length(map.xy.index) != 0){
for(i in 1:length(chr.xy)){
chr.ori[chr.ori == max.chr + i] <- chr.xy[i]
}
}
pvalueT <- as.matrix(Pmap[,-c(1:2)])
#print(dim(pvalueT))
pvalue.pos <- Pmap[, 2]
p0.index <- Pmap[, 1] == 0
if(sum(p0.index) != 0){
pvalue.pos[p0.index] <- 1:sum(p0.index)
}
pvalue.pos.list <- tapply(pvalue.pos, Pmap[, 1], list)
#scale the space parameter between chromosomes
if(!missing(band)){
band <- floor(band*(sum(sapply(pvalue.pos.list, max))/100))
}else{
band <- floor((sum(sapply(pvalue.pos.list, max))/100))
}
if(band==0) band=1
if(LOG10){
pvalueT[pvalueT <= 0] <- 1
pvalueT[pvalueT > 1] <- 1
}
#set the colors for the plot
#palette(heat.colors(1024)) #(heatmap)
#T=floor(1024/max(pvalue))
#plot(pvalue,pch=19,cex=0.6,col=(1024-floor(pvalue*T)))
#print(col)
if(is.vector(col)){
col <- matrix(col,R,length(col),byrow=TRUE)
}
if(is.matrix(col)){
#try to transform the colors into matrix for all traits
col <- matrix(as.vector(t(col)),R,dim(col)[2],byrow=TRUE)
}
Num <- as.numeric(table(Pmap[,1]))
Nchr <- length(Num)
N <- NULL
#print(Nchr)
#set the colors for each traits
for(i in 1:R){
colx <- col[i,]
colx <- colx[!is.na(colx)]
N[i] <- ceiling(Nchr/length(colx))
}
#insert the space into chromosomes and return the midpoint of each chromosome
ticks <- NULL
pvalue.posN <- NULL
#pvalue <- pvalueT[,j]
for(i in 0:(Nchr-1)){
if (i==0){
#pvalue <- append(pvalue,rep(Inf,band),after=0)
pvalue.posN <- pvalue.pos.list[[i+1]] + band
ticks[i+1] <- max(pvalue.posN)-floor(max(pvalue.pos.list[[i+1]])/2)
}else{
#pvalue <- append(pvalue,rep(Inf,band),after=sum(Num[1:i])+i*band)
pvalue.posN <- c(pvalue.posN, max(pvalue.posN) + band + pvalue.pos.list[[i+1]])
ticks[i+1] <- max(pvalue.posN)-floor(max(pvalue.pos.list[[i+1]])/2)
}
}
pvalue.posN.list <- tapply(pvalue.posN, Pmap[, 1], list)
#NewP[[j]] <- pvalue
#merge the pvalues of traits by column
if(LOG10){
logpvalueT <- -log10(pvalueT)
}else{
pvalueT <- abs(pvalueT)
logpvalueT <- pvalueT
}
add <- list()
for(i in 1:R){
colx <- col[i,]
colx <- colx[!is.na(colx)]
add[[i]] <- c(Num,rep(0,N[i]*length(colx)-Nchr))
}
TotalN <- max(pvalue.posN)
if(length(chr.den.col) > 1){
cir.density=TRUE
den.fold <- 20
density.list <- Densitplot(map=Pmap[,c(1,1,2)], col=chr.den.col, plot=FALSE, bin=bin.size, legend.max=bin.max)
#list(den.col=col.seg, legend.col=legend.col, legend.y=legend.y)
}else{
cir.density=FALSE
}
#print(dim(pvalueT))
if(is.null(xz)){
signal.line.index <- NULL
if(!is.null(threshold)){
if(!is.null(signal.line)){
for(l in 1:R){
if(LOG10){
signal.line.index <- c(signal.line.index,which(pvalueT[,l] < min(threshold)))
}else{
signal.line.index <- c(signal.line.index,which(pvalueT[,l] > max(threshold)))
}
}
signal.line.index <- unique(signal.line.index)
}
}
signal.lty=rep(2,length(signal.line.index))
}else{
signal.line.index=as.numeric(as.vector(xz[,1]))
signal.lty=as.numeric(as.vector(xz[,2]))
}#end is.null(xz)
signal.line.index <- pvalue.posN[signal.line.index]
}
if("c" %in% plot.type)
{
if(file.output){
if(file=="jpg") jpeg(paste("Circular-Manhattan.",paste(taxa,collapse="."),".jpg",sep=""), width = 8*dpi,height=8*dpi,res=dpi,quality = 100)
if(file=="pdf") pdf(paste("GAPIT.", taxa,".Circular.Manhattan.Plot.pdf" ,sep=""), width = 10,height=10)
if(file=="tiff") tiff(paste("Circular-Manhattan.",paste(taxa,collapse="."),".tiff",sep=""), width = 8*dpi,height=8*dpi,res=dpi)
}
if(!file.output){
if(!is.null(dev.list())) dev.new(width=8, height=8)
par(pty="s", xpd=TRUE, mar=c(1,1,1,1))
}
par(pty="s", xpd=TRUE, mar=c(1,1,1,1))
RR <- r+H*R+cir.band*R
if(cir.density){
plot(NULL,xlim=c(1.05*(-RR-4*cir.chr.h),1.1*(RR+4*cir.chr.h)),ylim=c(1.05*(-RR-4*cir.chr.h),1.1*(RR+4*cir.chr.h)),axes=FALSE,xlab="",ylab="")
}else{
plot(NULL,xlim=c(1.05*(-RR-4*cir.chr.h),1.05*(RR+4*cir.chr.h)),ylim=c(1.05*(-RR-4*cir.chr.h),1.05*(RR+4*cir.chr.h)),axes=FALSE,xlab="",ylab="")
}
if(!is.null(signal.line)){
if(!is.null(signal.line.index)){
X1chr <- (RR)*sin(2*pi*(signal.line.index-round(band/2))/TotalN)
Y1chr <- (RR)*cos(2*pi*(signal.line.index-round(band/2))/TotalN)
X2chr <- (r)*sin(2*pi*(signal.line.index-round(band/2))/TotalN)
Y2chr <- (r)*cos(2*pi*(signal.line.index-round(band/2))/TotalN)
#print(signal.line)
#print(dim(pvalueT))
#print(head(pvalueT))
#print(dim(xz))
#print(xz)
#print(head(pvalue.posN))
segments(X1chr,Y1chr,X2chr,Y2chr,lty=signal.lty,lwd=signal.line,col="grey")
}
}
for(i in 1:R){
#get the colors for each trait
colx <- col[i,]
colx <- colx[!is.na(colx)]
#debug
#print(colx)
#print(paste("Circular_Manhattan Plotting ",taxa[i],"...",sep=""))
pvalue <- pvalueT[,i]
logpvalue <- logpvalueT[,i]
if(is.null(ylim)){
if(LOG10){
Max <- ceiling(-log10(min(pvalue[pvalue!=0])))
}else{
Max <- ceiling(max(pvalue[pvalue!=Inf]))
if(Max<=1)
Max <- max(pvalue[pvalue!=Inf])
}
}else{
Max <- ylim[2]
}
Cpvalue <- (H*logpvalue/Max)
if(outward==TRUE){
if(cir.chr==TRUE){
#plot the boundary which represents the chromosomes
polygon.num <- 1000
#print(length(chr))
for(k in 1:length(chr)){
if(k==1){
polygon.index <- seq(round(band/2)+1,-round(band/2)+max(pvalue.posN.list[[1]]), length=polygon.num)
#change the axis from right angle into circle format
X1chr=(RR)*sin(2*pi*(polygon.index)/TotalN)
Y1chr=(RR)*cos(2*pi*(polygon.index)/TotalN)
X2chr=(RR+cir.chr.h)*sin(2*pi*(polygon.index)/TotalN)
Y2chr=(RR+cir.chr.h)*cos(2*pi*(polygon.index)/TotalN)
#print(length(X1chr))
if(is.null(chr.den.col)){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=rep(colx,ceiling(length(chr)/length(colx)))[k],border=rep(colx,ceiling(length(chr)/length(colx)))[k])
}else{
if(cir.density){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col="grey",border="grey")
}else{
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=chr.den.col,border=chr.den.col)
}
}
}else{
polygon.index <- seq(1+round(band/2)+max(pvalue.posN.list[[k-1]]),-round(band/2)+max(pvalue.posN.list[[k]]), length=polygon.num)
X1chr=(RR)*sin(2*pi*(polygon.index)/TotalN)
Y1chr=(RR)*cos(2*pi*(polygon.index)/TotalN)
X2chr=(RR+cir.chr.h)*sin(2*pi*(polygon.index)/TotalN)
Y2chr=(RR+cir.chr.h)*cos(2*pi*(polygon.index)/TotalN)
if(is.null(chr.den.col)){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=rep(colx,ceiling(length(chr)/length(colx)))[k],border=rep(colx,ceiling(length(chr)/length(colx)))[k])
}else{
if(cir.density){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col="grey",border="grey")
}else{
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=chr.den.col,border=chr.den.col)
}
}
}
}
if(cir.density){
segments(
(RR)*sin(2*pi*(pvalue.posN-round(band/2))/TotalN),
(RR)*cos(2*pi*(pvalue.posN-round(band/2))/TotalN),
(RR+cir.chr.h)*sin(2*pi*(pvalue.posN-round(band/2))/TotalN),
(RR+cir.chr.h)*cos(2*pi*(pvalue.posN-round(band/2))/TotalN),
col=density.list$den.col, lwd=0.1
)
legend(
x=RR+4*cir.chr.h,
y=(RR+4*cir.chr.h)/2,
horiz=F,
title="Density", legend=density.list$legend.y, pch=15, pt.cex = 3, col=density.list$legend.col,
cex=1, bty="n",
y.intersp=1,
x.intersp=1,
yjust=0.5, xjust=0, xpd=TRUE
)
}
# XLine=(RR+cir.chr.h)*sin(2*pi*(1:TotalN)/TotalN)
# YLine=(RR+cir.chr.h)*cos(2*pi*(1:TotalN)/TotalN)
# lines(XLine,YLine,lwd=1.5)
if(cir.density){
circle.plot(myr=RR+cir.chr.h,lwd=1.5,add=TRUE,col='grey')
circle.plot(myr=RR,lwd=1.5,add=TRUE,col='grey')
}else{
circle.plot(myr=RR+cir.chr.h,lwd=1.5,add=TRUE)
circle.plot(myr=RR,lwd=1.5,add=TRUE)
}
}
#plot the y axis of legend for each trait
if(cir.legend==TRUE){
#try to get the number after radix point
if(Max<=1) {
round.n=nchar(as.character(10^(-ceiling(-log10(Max)))))-1
}else{
round.n=1
}
segments(0,r+H*(i-1)+cir.band*(i-1),0,r+H*i+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
segments(0,r+H*(i-1)+cir.band*(i-1),H/20,r+H*(i-1)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-1)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.75)+cir.band*(i-1),H/20,r+H*(i-0.75)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.75)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.5)+cir.band*(i-1),H/20,r+H*(i-0.5)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.5)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.25)+cir.band*(i-1),H/20,r+H*(i-0.25)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.25)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0)+cir.band*(i-1),H/20,r+H*(i-0)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
#text(-r/15,r+H*(i-0.75)+cir.band*(i-1),round(Max*0.25,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
text(-r/15,r+H*(i-0.5)+cir.band*(i-1),round(Max*0.5,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
text(-r/15,r+H*(i-0.25)+cir.band*(i-1),round(Max*0.75,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
#text(-r/15,r+H*(i-0)+cir.band*(i-1),round(Max*1,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
#text(r/5,0.4*(i-1),taxa[i],adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
}
X=(Cpvalue+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(pvalue.posN-round(band/2))/TotalN)
Y=(Cpvalue+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(pvalue.posN-round(band/2))/TotalN)
# plot point in figure
points(X[1:(length(X)-legend.bit)],Y[1:(length(Y)-legend.bit)],pch=19,cex=cex[1],col=rep(rep(colx,N[i]),add[[i]]))
# plot significant line
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
for(thr in 1:length(threshold)){
significantline1=ifelse(LOG10, H*(-log10(threshold[thr]))/Max, H*(threshold[thr])/Max)
#s1X=(significantline1+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(0:TotalN)/TotalN)
#s1Y=(significantline1+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(0:TotalN)/TotalN)
# plot significant line
if(significantline1<H){
#lines(s1X,s1Y,type="l",col=threshold.col,lwd=threshold.col,lty=threshold.lty)
#if(thr==length(threshold))circle.plot(myr=(significantline1+r+H*(i-1)+cir.band*(i-1)),col="black",lwd=threshold.lwd[thr],lty=threshold.lty[thr])
#print("!!!!!")
circle.plot(myr=(significantline1+r+H*(i-1)+cir.band*(i-1)),col=threshold.col[thr],lwd=threshold.lwd[thr],lty=threshold.lty[thr])
#circle.plot(myr=(significantline1+r+H*(i-1)+cir.band*(i-1)),col="black",lwd=threshold.lwd[thr],lty=threshold.lty[thr])
}else{
warning(paste("No significant points for ",taxa[i]," pass the threshold level using threshold=",threshold[thr],"!",sep=""))
}
}
}
}
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
if(amplify==TRUE){
if(LOG10){
threshold <- sort(threshold)
significantline1=H*(-log10(max(threshold)))/Max
}else{
threshold <- sort(threshold, decreasing=TRUE)
significantline1=H*(min(threshold))/Max
}
p_amp.index <- which(Cpvalue>=significantline1)
HX1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
#cover the points that exceed the threshold with the color "white"
points(HX1,HY1,pch=19,cex=cex[1],col="white")
for(ll in 1:length(threshold)){
if(ll == 1){
if(LOG10){
significantline1=H*(-log10(threshold[ll]))/Max
}else{
significantline1=H*(threshold[ll])/Max
}
p_amp.index <- which(Cpvalue>=significantline1)
HX1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
}else{
if(LOG10){
significantline0=H*(-log10(threshold[ll-1]))/Max
significantline1=H*(-log10(threshold[ll]))/Max
}else{
significantline0=H*(threshold[ll-1])/Max
significantline1=H*(threshold[ll])/Max
}
p_amp.index <- which(Cpvalue>=significantline1 & Cpvalue < significantline0)
HX1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(Cpvalue[p_amp.index]+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
}
if(is.null(signal.col)){
# print(signal.pch)
points(HX1,HY1,pch=signal.pch,cex=signal.cex[ll]*cex[1],col=rep(rep(colx,N[i]),add[[i]])[p_amp.index])
}else{
# print(signal.pch)
points(HX1,HY1,pch=signal.pch,cex=signal.cex[ll]*cex[1],col=signal.col[ll])
}
}
}
}
}
if(cir.chr==TRUE){
ticks1=1.07*(RR+cir.chr.h)*sin(2*pi*(ticks-round(band/2))/TotalN)
ticks2=1.07*(RR+cir.chr.h)*cos(2*pi*(ticks-round(band/2))/TotalN)
if(is.null(chr.labels)){
#print(length(ticks))
for(i in 1:(length(ticks)-1)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.ori[i],srt=angle,font=2,cex=cex.axis)
}
}else{
for(i in 1:length(ticks)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.labels[i],srt=angle,font=2,cex=cex.axis)
}
}
}else{
ticks1=(0.9*r)*sin(2*pi*(ticks-round(band/2))/TotalN)
ticks2=(0.9*r)*cos(2*pi*(ticks-round(band/2))/TotalN)
if(is.null(chr.labels)){
for(i in 1:length(ticks)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.ori[i],srt=angle,font=2,cex=cex.axis)
}
}else{
for(i in 1:length(ticks)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.labels[i],srt=angle,font=2,cex=cex.axis)
}
}
}
}
if(outward==FALSE){
if(cir.chr==TRUE){
# XLine=(2*cir.band+RR+cir.chr.h)*sin(2*pi*(1:TotalN)/TotalN)
# YLine=(2*cir.band+RR+cir.chr.h)*cos(2*pi*(1:TotalN)/TotalN)
# lines(XLine,YLine,lwd=1.5)
polygon.num <- 1000
for(k in 1:length(chr)){
if(k==1){
polygon.index <- seq(round(band/2)+1,-round(band/2)+max(pvalue.posN.list[[1]]), length=polygon.num)
X1chr=(2*cir.band+RR)*sin(2*pi*(polygon.index)/TotalN)
Y1chr=(2*cir.band+RR)*cos(2*pi*(polygon.index)/TotalN)
X2chr=(2*cir.band+RR+cir.chr.h)*sin(2*pi*(polygon.index)/TotalN)
Y2chr=(2*cir.band+RR+cir.chr.h)*cos(2*pi*(polygon.index)/TotalN)
if(is.null(chr.den.col)){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=rep(colx,ceiling(length(chr)/length(colx)))[k],border=rep(colx,ceiling(length(chr)/length(colx)))[k])
}else{
if(cir.density){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col="grey",border="grey")
}else{
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=chr.den.col,border=chr.den.col)
}
}
}else{
polygon.index <- seq(1+round(band/2)+max(pvalue.posN.list[[k-1]]),-round(band/2)+max(pvalue.posN.list[[k]]), length=polygon.num)
X1chr=(2*cir.band+RR)*sin(2*pi*(polygon.index)/TotalN)
Y1chr=(2*cir.band+RR)*cos(2*pi*(polygon.index)/TotalN)
X2chr=(2*cir.band+RR+cir.chr.h)*sin(2*pi*(polygon.index)/TotalN)
Y2chr=(2*cir.band+RR+cir.chr.h)*cos(2*pi*(polygon.index)/TotalN)
if(is.null(chr.den.col)){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=rep(colx,ceiling(length(chr)/length(colx)))[k],border=rep(colx,ceiling(length(chr)/length(colx)))[k])
}else{
if(cir.density){
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col="grey",border="grey")
}else{
polygon(c(rev(X1chr),X2chr),c(rev(Y1chr),Y2chr),col=chr.den.col,border=chr.den.col)
}
}
}
}
if(cir.density){
segments(
(2*cir.band+RR)*sin(2*pi*(pvalue.posN-round(band/2))/TotalN),
(2*cir.band+RR)*cos(2*pi*(pvalue.posN-round(band/2))/TotalN),
(2*cir.band+RR+cir.chr.h)*sin(2*pi*(pvalue.posN-round(band/2))/TotalN),
(2*cir.band+RR+cir.chr.h)*cos(2*pi*(pvalue.posN-round(band/2))/TotalN),
col=density.list$den.col, lwd=0.1
)
legend(
x=RR+4*cir.chr.h,
y=(RR+4*cir.chr.h)/2,
title="Density", legend=density.list$legend.y, pch=15, pt.cex = 3, col=density.list$legend.col,
cex=1, bty="n",
y.intersp=1,
x.intersp=1,
yjust=0.5, xjust=0, xpd=TRUE
)
}
if(cir.density){
circle.plot(myr=2*cir.band+RR+cir.chr.h,lwd=1.5,add=TRUE,col='grey')
circle.plot(myr=2*cir.band+RR,lwd=1.5,add=TRUE,col='grey')
}else{
circle.plot(myr=2*cir.band+RR+cir.chr.h,lwd=1.5,add=TRUE)
circle.plot(myr=2*cir.band+RR,lwd=1.5,add=TRUE)
}
}
if(cir.legend==TRUE){
#try to get the number after radix point
if(Max<=1) {
round.n=nchar(as.character(10^(-ceiling(-log10(Max)))))-1
}else{
round.n=2
}
segments(0,r+H*(i-1)+cir.band*(i-1),0,r+H*i+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
segments(0,r+H*(i-1)+cir.band*(i-1),H/20,r+H*(i-1)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-1)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.75)+cir.band*(i-1),H/20,r+H*(i-0.75)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.75)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.5)+cir.band*(i-1),H/20,r+H*(i-0.5)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.5)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0.25)+cir.band*(i-1),H/20,r+H*(i-0.25)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0.25)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
segments(0,r+H*(i-0)+cir.band*(i-1),H/20,r+H*(i-0)+cir.band*(i-1),col=cir.legend.col,lwd=1.5)
circle.plot(myr=r+H*(i-0)+cir.band*(i-1),lwd=0.5,add=TRUE,col='grey')
text(-r/15,r+H*(i-0.25)+cir.band*(i-1),round(Max*0.25,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
#text(-r/15,r+H*(i-0.5)+cir.band*(i-1),round(Max*0.5,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
text(-r/15,r+H*(i-0.75)+cir.band*(i-1),round(Max*0.75,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
#text(-r/15,r+H*(i-1)+cir.band*(i-1),round(Max*1,round.n),adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
#text(r,0.4*(i-1),taxa[i],adj=1,col=cir.legend.col,cex=cir.legend.cex,font=2)
}
X=(-Cpvalue+r+H*i+cir.band*(i-1))*sin(2*pi*(pvalue.posN-round(band/2))/TotalN)
Y=(-Cpvalue+r+H*i+cir.band*(i-1))*cos(2*pi*(pvalue.posN-round(band/2))/TotalN)
#points(X,Y,pch=19,cex=cex[1],col=rep(rep(colx,N[i]),add[[i]]))
points(X[1:(length(X)-legend.bit)],Y[1:(length(Y)-legend.bit)],pch=19,cex=cex[1],col=rep(rep(colx,N[i]),add[[i]]))
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
for(thr in 1:length(threshold)){
significantline1=ifelse(LOG10, H*(-log10(threshold[thr]))/Max, H*(threshold[thr])/Max)
#s1X=(significantline1+r+H*(i-1)+cir.band*(i-1))*sin(2*pi*(0:TotalN)/TotalN)
#s1Y=(significantline1+r+H*(i-1)+cir.band*(i-1))*cos(2*pi*(0:TotalN)/TotalN)
if(significantline1<H){
#lines(s1X,s1Y,type="l",col=threshold.col,lwd=threshold.col,lty=threshold.lty)
circle.plot(myr=(-significantline1+r+H*i+cir.band*(i-1)),col=threshold.col[thr],lwd=threshold.lwd[thr],lty=threshold.lty[thr])
}else{
warning(paste("No significant points for ",taxa[i]," pass the threshold level using threshold=",threshold[thr],"!",sep=""))
}
}
if(amplify==TRUE){
if(LOG10){
threshold <- sort(threshold)
significantline1=H*(-log10(max(threshold)))/Max
}else{
threshold <- sort(threshold, decreasing=TRUE)
significantline1=H*(min(threshold))/Max
}
p_amp.index <- which(Cpvalue>=significantline1)
HX1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
#cover the points that exceed the threshold with the color "white"
points(HX1,HY1,pch=19,cex=cex[1],col="white")
for(ll in 1:length(threshold)){
if(ll == 1){
if(LOG10){
significantline1=H*(-log10(threshold[ll]))/Max
}else{
significantline1=H*(threshold[ll])/Max
}
p_amp.index <- which(Cpvalue>=significantline1)
HX1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
}else{
if(LOG10){
significantline0=H*(-log10(threshold[ll-1]))/Max
significantline1=H*(-log10(threshold[ll]))/Max
}else{
significantline0=H*(threshold[ll-1])/Max
significantline1=H*(threshold[ll])/Max
}
p_amp.index <- which(Cpvalue>=significantline1 & Cpvalue < significantline0)
HX1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*sin(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
HY1=(-Cpvalue[p_amp.index]+r+H*i+cir.band*(i-1))*cos(2*pi*(pvalue.posN[p_amp.index]-round(band/2))/TotalN)
}
if(is.null(signal.col)){
points(HX1,HY1,pch=signal.pch,cex=signal.cex[ll]*cex[1],col=rep(rep(colx,N[i]),add[[i]])[p_amp.index])
}else{
points(HX1,HY1,pch=signal.pch,cex=signal.cex[ll]*cex[1],col=signal.col[ll])
}
}
}
}
}
if(cir.chr==TRUE){
ticks1=1.1*(2*cir.band+RR)*sin(2*pi*(ticks-round(band/2))/TotalN)
ticks2=1.1*(2*cir.band+RR)*cos(2*pi*(ticks-round(band/2))/TotalN)
if(is.null(chr.labels)){
for(i in 1:(length(ticks)-1)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.ori[i],srt=angle,font=2,cex=cex.axis)
}
}else{
for(i in 1:length(ticks)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.labels[i],srt=angle,font=2,cex=cex.axis)
}
}
}else{
ticks1=1.0*(RR+cir.band)*sin(2*pi*(ticks-round(band/2))/TotalN)
ticks2=1.0*(RR+cir.band)*cos(2*pi*(ticks-round(band/2))/TotalN)
if(is.null(chr.labels)){
for(i in 1:length(ticks)){
#adjust the angle of labels of circle plot
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.ori[i],srt=angle,font=2,cex=cex.axis)
}
}else{
for(i in 1:length(ticks)){
angle=360*(1-(ticks-round(band/2))[i]/TotalN)
text(ticks1[i],ticks2[i],chr.labels[i],srt=angle,font=2,cex=cex.axis)
}
}
}
}
}
taxa=append("Centre",taxa,)
taxa_col=rep("black",R)
taxa_col=append("red",taxa_col)
for(j in 1:(R+1)){
text(r/5,0.4*(j-1),taxa[j],adj=1,col=taxa_col[j],cex=cir.legend.cex,font=2)
}
taxa=taxa[-1]
if(file.output) dev.off()
}
if("q" %in% plot.type){
#print("Starting QQ-plot!",quote=F)
amplify=FALSE
if(multracks){
if(file.output){
if(file=="jpg") jpeg(paste("Multracks.QQ_plot.",paste(taxa,collapse="."),".jpg",sep=""), width = R*2.5*dpi,height=5.5*dpi,res=dpi,quality = 100)
if(file=="pdf") pdf(paste("Multracks.QQ_plot.",paste(taxa,collapse="."),".pdf",sep=""), width = R*2.5,height=5.5)
if(file=="tiff") tiff(paste("Multracks.QQ_plot.",paste(taxa,collapse="."),".tiff",sep=""), width = R*2.5*dpi,height=5.5*dpi,res=dpi)
par(mfcol=c(1,R),mar = c(0,1,4,1.5),oma=c(3,5,0,0),xpd=TRUE)
}else{
if(is.null(dev.list())) dev.new(width = 2.5*R, height = 5.5)
par(xpd=TRUE)
}
for(i in 1:R){
print(paste("Multracks_QQ Plotting ",taxa[i],"...",sep=""))
P.values=as.numeric(Pmap[,i+2])
P.values=P.values[!is.na(P.values)]
if(LOG10){
P.values=P.values[P.values>0]
P.values=P.values[P.values<=1]
N=length(P.values)
P.values=P.values[order(P.values)]
}else{
N=length(P.values)
P.values=P.values[order(P.values,decreasing=TRUE)]
}
p_value_quantiles=(1:length(P.values))/(length(P.values)+1)
log.Quantiles <- -log10(p_value_quantiles)
if(LOG10){
log.P.values <- -log10(P.values)
}else{
log.P.values <- P.values
}
#calculate the confidence interval of QQ-plot
if(conf.int){
N1=length(log.Quantiles)
c95 <- rep(NA,N1)
c05 <- rep(NA,N1)
for(j in 1:N1){
xi=ceiling((10^-log.Quantiles[j])*N)
if(xi==0)xi=1
c95[j] <- qbeta(0.95,xi,N-xi+1)
c05[j] <- qbeta(0.05,xi,N-xi+1)
}
index=length(c95):1
}else{
c05 <- 1
c95 <- 1
}
YlimMax <- max(floor(max(max(-log10(c05)), max(-log10(c95)))+1), floor(max(log.P.values)+1))
plot(NULL, xlim = c(0,floor(max(log.Quantiles)+1)), axes=FALSE, cex.axis=cex.axis, cex.lab=1.2,ylim=c(0,YlimMax),xlab ="", ylab="", main = taxa[i])
axis(1, at=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), labels=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), cex.axis=cex.axis)
axis(2, at=seq(0,YlimMax,ceiling(YlimMax/10)), labels=seq(0,YlimMax,ceiling(YlimMax/10)), cex.axis=cex.axis)
#plot the confidence interval of QQ-plot
if(conf.int) polygon(c(log.Quantiles[index],log.Quantiles),c(-log10(c05)[index],-log10(c95)),col=conf.int.col,border=conf.int.col)
if(!is.null(threshold.col)){par(xpd=FALSE); abline(a = 0, b = 1, col = threshold.col[1],lwd=2); par(xpd=TRUE)}
points(log.Quantiles, log.P.values, col = col[1],pch=1,cex=cex[3])
#print(max(log.Quantiles))
# print(length(log.Quantiles))
# print(length(log.P.values))
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
thre.line=-log10(min(threshold))
if(amplify==TRUE){
thre.index=which(log.P.values>=thre.line)
if(length(thre.index)!=0){
#cover the points that exceed the threshold with the color "white"
points(log.Quantiles[thre.index],log.P.values[thre.index], col = "white",pch=19,cex=cex[3])
if(is.null(signal.col)){
points(log.Quantiles[thre.index],log.P.values[thre.index],col = col[1],pch=signal.pch[1],cex=signal.cex[1])
}else{
points(log.Quantiles[thre.index],log.P.values[thre.index],col = signal.col[1],pch=signal.pch[1],cex=signal.cex[1])
}
}
}
}
}
}
if(box) box()
if(file.output) dev.off()
if(R > 1){
#qq_col=rainbow(R)
qq_col=rep(c( '#FF6A6A', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(R/5))
signal.col <- NULL
if(file.output){
if(file=="jpg") jpeg(paste("Multiple.QQ_plot.",paste(taxa,collapse="."),".jpg",sep=""), width = 5.5*dpi,height=5.5*dpi,res=dpi,quality = 100)
if(file=="pdf") pdf(paste("Multiple.QQ_plot.",paste(taxa,collapse="."),".pdf",sep=""), width = 5.5,height=5.5)
if(file=="tiff") tiff(paste("Multiple.QQ_plot.",paste(taxa,collapse="."),".tiff",sep=""), width = 5.5*dpi,height=5.5*dpi,res=dpi)
par(mar = c(5,5,4,2),xpd=TRUE)
}else{
dev.new(width = 5.5, height = 5.5)
par(xpd=TRUE)
}
P.values=as.numeric(Pmap[,i+2])
P.values=P.values[!is.na(P.values)]
if(LOG10){
P.values=P.values[P.values>0]
P.values=P.values[P.values<=1]
N=length(P.values)
P.values=P.values[order(P.values)]
}else{
N=length(P.values)
P.values=P.values[order(P.values,decreasing=TRUE)]
}
p_value_quantiles=(1:length(P.values))/(length(P.values)+1)
log.Quantiles <- -log10(p_value_quantiles)
# calculate the confidence interval of QQ-plot
if(conf.int){
N1=length(log.Quantiles)
c95 <- rep(NA,N1)
c05 <- rep(NA,N1)
for(j in 1:N1){
xi=ceiling((10^-log.Quantiles[j])*N)
if(xi==0)xi=1
c95[j] <- qbeta(0.95,xi,N-xi+1)
c05[j] <- qbeta(0.05,xi,N-xi+1)
}
index=length(c95):1
}
if(!conf.int){c05 <- 1; c95 <- 1}
Pmap.min <- Pmap[,3:(R+2)]
YlimMax <- max(floor(max(max(-log10(c05)), max(-log10(c95)))+1), -log10(min(Pmap.min[Pmap.min > 0])))
plot(NULL, xlim = c(0,floor(max(log.Quantiles)+1)), axes=FALSE, cex.axis=cex.axis, cex.lab=1.2,ylim=c(0, floor(YlimMax+1)),xlab =expression(Expected~~-log[10](italic(p))), ylab = expression(Observed~~-log[10](italic(p))), main = "QQ plot")
#legend("topleft",taxa,col=t(col)[1:R],pch=1,pt.lwd=2,text.font=6,box.col=NA)
legend("topleft",taxa,col=qq_col[1:R],pch=1,pt.lwd=3,text.font=6,box.col=NA)
axis(1, at=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), labels=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), cex.axis=cex.axis)
axis(2, at=seq(0,floor(YlimMax+1),ceiling((YlimMax+1)/10)), labels=seq(0,floor((YlimMax+1)),ceiling((YlimMax+1)/10)), cex.axis=cex.axis)
#print(log.Quantiles[index])
#print(index)
#print(length(log.Quantiles))
# plot the confidence interval of QQ-plot
if(conf.int) polygon(c(log.Quantiles[index],log.Quantiles),c(-log10(c05)[index],-log10(c95)),col=conf.int.col,border=conf.int.col)
for(i in 1:R){
#print(paste("Multraits_QQ Plotting ",taxa[i],"...",sep=""))
P.values=as.numeric(Pmap[,i+2])
P.values=P.values[!is.na(P.values)]
if(LOG10){
P.values=P.values[P.values>0]
P.values=P.values[P.values<=1]
N=length(P.values)
P.values=P.values[order(P.values)]
}else{
N=length(P.values)
P.values=P.values[order(P.values,decreasing=TRUE)]
}
p_value_quantiles=(1:length(P.values))/(length(P.values)+1)
log.Quantiles <- -log10(p_value_quantiles)
if(LOG10){
log.P.values <- -log10(P.values)
}else{
log.P.values <- P.values
}
if((i == 1) & !is.null(threshold.col)){par(xpd=FALSE); abline(a = 0, b = 1, col = threshold.col[1],lwd=2); par(xpd=TRUE)}
#print(length(log.Quantiles))
#print("!!!!!")
#points(log.Quantiles, log.P.values, col = t(col)[i],pch=1,lwd=3,cex=cex[3])
points(log.Quantiles, log.P.values, col = qq_col[i],pch=1,lwd=3,cex=cex[3])
#print(max(log.Quantiles))
#
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
thre.line=-log10(min(threshold))
if(amplify==TRUE){
thre.index=which(log.P.values>=thre.line)
if(length(thre.index)!=0){
# cover the points that exceed the threshold with the color "white"
points(log.Quantiles[thre.index],log.P.values[thre.index], col = "white",pch=19,lwd=3,cex=cex[3])
if(is.null(signal.col)){
points(log.Quantiles[thre.index],log.P.values[thre.index],col = t(col)[i],pch=signal.pch[1],cex=signal.cex[1])
}else{
points(log.Quantiles[thre.index],log.P.values[thre.index],col = signal.col[1],pch=signal.pch[1],cex=signal.cex[1])
}
}
}
}
}
}
box()
if(file.output) dev.off()
}
}else{
for(i in 1:R){
print(paste("Q_Q Plotting ",taxa[i],"...",sep=""))
if(file.output){
if(file=="jpg") jpeg(paste("QQplot.",taxa[i],".jpg",sep=""), width = 5.5*dpi,height=5.5*dpi,res=dpi,quality = 100)
if(file=="pdf") pdf(paste("QQplot.",taxa[i],".pdf",sep=""), width = 5.5,height=5.5)
if(file=="tiff") tiff(paste("QQplot.",taxa[i],".tiff",sep=""), width = 5.5*dpi,height=5.5*dpi,res=dpi)
par(mar = c(5,5,4,2),xpd=TRUE)
}else{
if(is.null(dev.list())) dev.new(width = 5.5, height = 5.5)
par(xpd=TRUE)
}
P.values=as.numeric(Pmap[,i+2])
P.values=P.values[!is.na(P.values)]
if(LOG10){
P.values=P.values[P.values>0]
P.values=P.values[P.values<=1]
N=length(P.values)
P.values=P.values[order(P.values)]
}else{
N=length(P.values)
P.values=P.values[order(P.values,decreasing=TRUE)]
}
p_value_quantiles=(1:length(P.values))/(length(P.values)+1)
log.Quantiles <- -log10(p_value_quantiles)
if(LOG10){
log.P.values <- -log10(P.values)
}else{
log.P.values <- P.values
}
#calculate the confidence interval of QQ-plot
if(conf.int){
N1=length(log.Quantiles)
c95 <- rep(NA,N1)
c05 <- rep(NA,N1)
for(j in 1:N1){
xi=ceiling((10^-log.Quantiles[j])*N)
if(xi==0)xi=1
c95[j] <- qbeta(0.95,xi,N-xi+1)
c05[j] <- qbeta(0.05,xi,N-xi+1)
}
index=length(c95):1
}else{
c05 <- 1
c95 <- 1
}
#print(max(log.Quantiles))
#print("@@@@@")
YlimMax <- max(floor(max(max(-log10(c05)), max(-log10(c95)))+1), floor(max(log.P.values)+1))
plot(NULL, xlim = c(0,floor(max(log.Quantiles)+1)), axes=FALSE, cex.axis=cex.axis, cex.lab=1.2,ylim=c(0,YlimMax),xlab =expression(Expected~~-log[10](italic(p))), ylab = expression(Observed~~-log[10](italic(p))), main = paste("QQplot of",taxa[i]))
axis(1, at=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), labels=seq(0,floor(max(log.Quantiles)+1),ceiling((max(log.Quantiles)+1)/10)), cex.axis=cex.axis)
axis(2, at=seq(0,YlimMax,ceiling(YlimMax/10)), labels=seq(0,YlimMax,ceiling(YlimMax/10)), cex.axis=cex.axis)
#plot the confidence interval of QQ-plot
#print(log.Quantiles[index])
qq_col=rainbow(R)
#if(conf.int) polygon(c(log.Quantiles[index],log.Quantiles),c(-log10(c05)[index],-log10(c95)),col=conf.int.col,border=conf.int.col)
if(conf.int) polygon(c(log.Quantiles[index],log.Quantiles),c(-log10(c05)[index],-log10(c95)),col=qq_col[i],border=conf.int.col)
if(!is.null(threshold.col)){par(xpd=FALSE); abline(a = 0, b = 1, col = threshold.col[1],lwd=2); par(xpd=TRUE)}
points(log.Quantiles, log.P.values, col = col[1],pch=19,cex=2)
if(!is.null(threshold)){
if(sum(threshold!=0)==length(threshold)){
thre.line=-log10(min(threshold))
if(amplify==TRUE){
thre.index=which(log.P.values>=thre.line)
if(length(thre.index)!=0){
#print("!!!!")
#cover the points that exceed the threshold with the color "white"
points(log.Quantiles[thre.index],log.P.values[thre.index], col = "white",pch=19,lwd=3,cex=cex[3])
if(is.null(signal.col)){
points(log.Quantiles[thre.index],log.P.values[thre.index],col = col[1],pch=signal.pch[1],cex=signal.cex[1])
}else{
points(log.Quantiles[thre.index],log.P.values[thre.index],col = signal.col[1],pch=signal.pch[1],cex=signal.cex[1])
}
}
}
}
}
box()
if(file.output) dev.off()
}
}
print("Multiple QQ plot has been finished!",quote=F)
}
}#End of Whole function
#}
`GAPIT.Compress` <-
function(KI,kinship.cluster = "average",kinship.group = "Mean",GN=nrow(KI),Timmer,Memory){
#Object: To cluster individuals into groups based on kinship
#Output: GA, KG
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: April 14, 2011
##############################################################################################
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP start")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp start")
# Extract the line names
line.names <- KI[,1]
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Does this change memory0")
Memory=GAPIT.Memory(Memory=Memory,Infor="Does this change memory0")
# Remove the first column of the kinship matrix, which is the line names
KI <- KI[ ,-1]
# Convert kinship to distance
#distance.matrix <- 2 - KI
#distance.matrix.as.dist <- as.dist(distance.matrix)
#distance.matrix.as.dist <- as.dist(2 - KI)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP distance")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp distance")
#print(paste("The value of kinship.cluster is ", kinship.cluster, sep = ""))
# hclust() will perform the hiearchical cluster analysis
#cluster.distance.matrix <- hclust(distance.matrix.as.dist, method = kinship.cluster)
#cluster.distance.matrix <- hclust(as.dist(2 - KI), method = kinship.cluster)
distance.matrix=dist(KI,upper=TRUE) #Jiabo Wang modified ,the dist is right function for cluster
cluster.distance.matrix=hclust(distance.matrix,method=kinship.cluster)
#cutree(out_hclust,k=3)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP cluster")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp cluster")
# Cutree will assign lines into k clusters
group.membership <- cutree(cluster.distance.matrix, k = GN)
compress_z=table(group.membership,paste(line.names)) #build compress z with group.membership
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP cutree")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp cutree")
#calculate group kinship
if(kinship.group == "Mean"){
#This matrix ooperation is much faster than tapply function for "Mean"
x=as.factor(group.membership)
#b = model.matrix(~x-1)
n=max(as.numeric(as.vector(x)))
b=diag(n)[x,]
KG=t(b)%*%as.matrix(KI)%*%b
CT=t(b)%*%(0*as.matrix(KI)+1)%*%b
KG=as.matrix(KG/CT)
rownames(KG)=c(1:nrow(KG))
colnames(KG)=c(1:ncol(KG))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP calculation original")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp calculation original")
}else{
gm=as.factor(group.membership)
kv=as.numeric(as.matrix(KI))
kvr=rep(gm,ncol(KI))
kvc=as.numeric(t(matrix(kvr,nrow(KI),ncol(KI))))
kInCol=t(rbind(kv,kvr,kvc))
rm(gm)
rm(kv)
rm(kvr)
rm(kvc)
rm(KI)
gc()
#This part does not work yet
#if(kinship.group == "Mean")
# KG<- tapply(kInCol[,1], list(kInCol[,2], kInCol[,3]), mean)
if(kinship.group == "Max")
KG <- tapply(kInCol[,1], list(kInCol[,2], kInCol[,3]), max)
if(kinship.group == "Min")
KG <- tapply(kInCol[,1], list(kInCol[,2], kInCol[,3]), min)
if(kinship.group == "Median")
KG <- tapply(kInCol[,1], list(kInCol[,2], kInCol[,3]), median)
} #this is end of brancing "Mean" and the rest
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP calculation")
Memory=GAPIT.Memory(Memory=Memory,Infor="cp calculation")
# add line names
#GA <- data.frame(group.membership)
GA <- data.frame(cbind(as.character(line.names),as.numeric(group.membership) ))
#Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="CP Final")
#Memory=GAPIT.Memory(Memory=Memory,Infor="CP Final")
#write.table(KG, paste("KG_from_", kinship.group, "_Method.txt"), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
#print("GAPIT.Compress accomplished successfully!")
return(list(GA=GA, KG=KG,Timmer=Timmer,Memory=Memory))
}#The function GAPIT.Compress ends here
#=============================================================================================
`GAPIT.Compression.Visualization` <-
function(Compression = Compression, name.of.trait = name.of.trait){
#Object: Conduct the Benjamini-Hochberg FDR-Controlling Procedure
#Output: Three pdfs: One of the log likelihood function, one of the genetic and error variance component,
# and one of the heritabilities
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: May 10, 2011
##############################################################################################
#Graph the optimum compression
print("GAPIT.Compression.Visualization")
#print(Compression)
if(length(Compression)<=6) Compression=t(as.matrix(Compression[which(Compression[,4]!="NULL" | Compression[,4]!="NaN"),]))
if(length(Compression)==6) Compression=matrix(Compression,1,6)
#print("Compression matrix")
#print(Compression)
#print(length(Compression) )
if(length(Compression)>6) Compression=Compression[which(Compression[,4]!="NULL" | Compression[,4]!="NaN"),]
if(length(Compression)<1) return() #no result
#Pie chart for the optimum setting
#-------------------------------------------------------------------------------
print("Pie chart")
LL=as.numeric(Compression[,4])
Compression.best=Compression[1,]
variance=as.numeric(Compression.best[5:6])
#colors <- c("grey50","grey70")
colors <- c("#990000","dimgray")
varp=variance/sum(variance)
h2.opt= varp[1]
labels0 <- round(varp * 100, 1)
labels <- paste(labels0, "%", sep="")
legend0=c("Genetic: ","Residual: ")
legend <- paste(legend0, round(variance*100)/100, sep="")
LL.best0=as.numeric(Compression.best[4] )
LL.best=paste("-2LL: ",floor(LL.best0*100)/100,sep="")
label.comp=paste(c("Cluster method: ","Group method: ","Group number: "), Compression.best[c(1:3)], sep="")
theOptimum=c(label.comp,LL.best)
#print(variance)
pdf(paste("GAPIT.", name.of.trait,".Optimum.pdf", sep = ""), width = 14)
par(mfrow = c(1,1), mar = c(1,1,5,5), lab = c(5,5,7))
pie(variance, col=colors, labels=labels,angle=45,border=NA)
legend(1.0, 0.5, legend, cex=1.5, bty="n",
fill=colors)
#Display the optimum compression
text(1.5,.0, "The optimum compression", col= "gray10")
for(i in 1:4){
text(1.5,-.1*i, theOptimum[i], col= "gray10")
}
dev.off()
#sort Compression by group number for plot order
Compression=Compression[order(as.numeric(Compression[,3])),]
#Graph compression with multiple groups
#print("Graph compression with multiple groups")
if(length(Compression)==6) return() #For to exit if only one row
#print("It should not go here")
if(length(unique(Compression[,3]))>1)
{
#Create a vector of colors
#print("Setting colors")
color.vector.basic <- c("red","blue","black", "blueviolet","indianred","cadetblue","orange")
color.vector.addition <- setdiff(c(colors()[grep("red",colors())], colors()[grep("blue",colors())]),color.vector.basic )
color.vector.addition.mixed <- sample(color.vector.addition,max(0,((length(unique(Compression[,1])) * length(unique(Compression[,2])))-length(color.vector.basic))))
color.vector <- c(color.vector.basic,color.vector.addition.mixed )
#Create a vector of numbers for the line dot types
line.vector <- rep(1:(length(unique(Compression[,1])) * length(unique(Compression[,2]))))
#We want to have a total of three plots, one displaying the likelihood function, one displaying the variance components, and one displaying the
# heritability
pdf(paste("GAPIT.", name.of.trait,".Compression.multiple.group", ".pdf", sep = ""), width = 14)
par(mfrow = c(2,3), mar = c(5,5,1,1), lab = c(5,5,7))
# Make the likelihood function plot
#print("Likelihood")
k <- 1
for(i in 1:length(unique(Compression[,1]))){
for(j in 1:length(unique(Compression[,2]))){
if((i == 1)&(j == 1)) {
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,4])
plot(y~x,type="l", pch = 30, lty = line.vector[i], ylim=c(min(as.numeric(Compression[,4])),max(as.numeric(Compression[,4]))), xlim = c(min(as.numeric(Compression[,3])),max(as.numeric(Compression[,3]))),
col = color.vector[j], xlab = "Number of Groups", ylab = "-2Log Likelihoood",lwd=1 )
label = paste(c(as.character(unique(Compression[,1]))[k]," ",as.character(unique(Compression[,2]))[j]), collapse = "")
}
if((i != 1)|(j != 1)) {
k <- k+1
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,4])
lines(y~x,type="l", pch = 30, lty = line.vector[i], col = color.vector[j])
label = c(label, paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = ""))
}
}
}
#Make a legend
#legend("topright", label, fill = color.vector)
legend.col= 1+floor(length(unique(Compression[,1])) * length(unique(Compression[,2]))/20)
line.style=rep(1:length(unique(Compression[,1])), each = length(unique(Compression[,2])))
line.color=rep(1:length(unique(Compression[,2])), length(unique(Compression[,1])))
legend("topright", label, col = color.vector[line.color], lty = line.style, ncol=legend.col,horiz=FALSE,bty="n")
# Make the genetic variance component plots
#print("genetic variance")
k <- 1
for(i in 1:length(unique(Compression[,1]))){
for(j in 1:length(unique(Compression[,2]))){
if((i == 1)&(j == 1)) {
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,5])
plot(y~x,type="l", pch = 17, lty = line.vector[i], ylim=c(min(as.numeric(Compression[,5])),max(as.numeric(Compression[,5]))), xlim = c(min(as.numeric(Compression[,3])),max(as.numeric(Compression[,3]))),
col = color.vector[j], xlab = "Number of Groups", ylab = "Genetic Variance", )
#label = paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = "")
}
if((i != 1)|(j != 1)) {
k <- k+1
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,5])
lines(y~x,type="l", pch = 17, lty = line.vector[i], col = color.vector[j])
#label = c(label, paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = ""))
}
}
}
#Make a legend
#legend("topleft", label, fill = color.vector)
# Make the residual variance component plots
k <- 1
for(i in 1:length(unique(Compression[,1]))){
for(j in 1:length(unique(Compression[,2]))){
if((i == 1)&(j == 1)) {
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,6])
plot(y~x,type="l", pch = 17, ylim=c(min(as.numeric(Compression[,6])),max(as.numeric(Compression[,6]))), xlim = c(min(as.numeric(Compression[,3])),max(as.numeric(Compression[,3]))),
col = color.vector[j], xlab = "Number of Groups", ylab = "Residual Variance", )
#label = paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = "")
}
if((i != 1)|(j != 1)) {
k <- k+1
Compression.subset <- Compression[which( (Compression[,1] == as.character(unique(Compression[,1])[i])) & (Compression[,2] == as.character(unique(Compression[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,6])
lines(y~x,type="l", pch = 17, lty = line.vector[i], col = color.vector[j])
#label = c(label, paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = ""))
}
}
}
#Make a legend
#legend("topright", label, fill = color.vector)
#calculate total variance and h2
#print("h2")
heritablilty.vector <- as.numeric(Compression[,5])/(as.numeric(Compression[,5]) + as.numeric(Compression[,6]))
totalVariance.vector <- as.numeric(as.numeric(Compression[,5]) + as.numeric(Compression[,6]))
Compression.h2 <- cbind(Compression, heritablilty.vector,totalVariance.vector)
# Make the total variance component plots
#print("Total variance")
k <- 1
for(i in 1:length(unique(Compression.h2[,1]))){
for(j in 1:length(unique(Compression.h2[,2]))){
if((i == 1)&(j == 1)) {
Compression.subset <- Compression.h2[which( (Compression.h2[,1] == as.character(unique(Compression.h2[,1])[i])) & (Compression.h2[,2] == as.character(unique(Compression.h2[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,8])
plot(y~x,type="l", pch = 17, lty = line.vector[k], ylim=c(min(as.numeric(Compression.h2[,8])),max(as.numeric(Compression.h2[,8]))), xlim = c(min(as.numeric(Compression.h2[,3])),max(as.numeric(Compression.h2[,3]))),
col = color.vector[1], xlab = "Number of Groups", ylab = "Total Variance", )
#label = paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = "")
}
if((i != 1)|(j != 1)) {
k <- k+1
Compression.subset <- Compression.h2[which( (Compression.h2[,1] == as.character(unique(Compression.h2[,1])[i])) & (Compression.h2[,2] == as.character(unique(Compression.h2[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,8])
lines(y~x,type="l", pch = 17, lty = line.vector[i], col = color.vector[j])
#label = c(label, paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = ""))
}
}
}
#Make a legend
#legend("topright", label, fill = color.vector)
# Make the heritability plots
#print("h2 plot")
k <- 1
for(i in 1:length(unique(Compression[,1]))){
for(j in 1:length(unique(Compression[,2]))){
if((i == 1)&(j == 1)) {
Compression.subset <- Compression.h2[which( (Compression.h2[,1] == as.character(unique(Compression.h2[,1])[i])) & (Compression.h2[,2] == as.character(unique(Compression.h2[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,7])
plot(y~x,type="l", pch = 17, lty = line.vector[k], ylim=c(min(as.numeric(Compression.h2[,7])),max(as.numeric(Compression.h2[,7]))), xlim = c(min(as.numeric(Compression.h2[,3])),max(as.numeric(Compression.h2[,3]))),
col = color.vector[1], xlab = "Number of Groups", ylab = "Heritability", )
#label = paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = "")
}
if((i != 1)|(j != 1)) {
k <- k+1
Compression.subset <- Compression.h2[which( (Compression.h2[,1] == as.character(unique(Compression.h2[,1])[i])) & (Compression.h2[,2] == as.character(unique(Compression.h2[,2])[j])) ), ]
x <- as.numeric(Compression.subset[,3])
y <- as.numeric(Compression.subset[,7])
lines(y~x,type="l", lty = line.vector[i], pch = 17, col = color.vector[j])
#label = c(label, paste(c(as.character(unique(Compression[,1]))[i]," ",as.character(unique(Compression[,2]))[j]), collapse = ""))
}
}
}
#Make a legend
#legend("topleft", label, fill = color.vector)
legend.col= 1+floor(length(unique(Compression[,1])) * length(unique(Compression[,2]))/20)
line.style=rep(1:length(unique(Compression[,1])), each = length(unique(Compression[,2])))
line.color=rep(1:length(unique(Compression[,2])), length(unique(Compression[,1])))
# Make labels
plot(0~0,axes=FALSE,type="l",ylab = "",xlab = "",frame.plot=FALSE)
legend("topleft", label, col = color.vector[line.color], lty = line.style, ncol=legend.col,horiz=FALSE)
dev.off()
}#end of Graph compression with multiple groups
#Graph compression with single groups
#print("Graph compression with single groups")
if(length(unique(Compression[,3]))==1& length(unique(Compression[,1]))*length(unique(Compression[,2]))>1)
{
#Graph the compression with only one group
pdf(paste("GAPIT.Compression.single.group.", name.of.trait, ".pdf", sep = ""), width = 14)
par(mfrow = c(2,2), mar = c(5,5,1,1), lab = c(5,5,7))
nkt=length(unique(Compression[,1]))
nca=length(unique(Compression[,2]))
kvr=rep(c(1:nkt),nca)
kvc0=rep(c(1:nca),nkt)
kvc=as.numeric(t(matrix(kvc0,nca,nkt)))
kt.name=Compression[1:nkt,1]
ca.index=((1:nca)-1)*nkt+1
ca.name=Compression[ca.index,2]
KG<- t(tapply(as.numeric(Compression[,4]), list(kvr, kvc), mean))
colnames(KG)=kt.name
barplot(as.matrix(KG), ylab= "-2 Log Likelihood",beside=TRUE, col=rainbow(length(unique(Compression[,2]))))
KG<- t(tapply(as.numeric(Compression[,5]), list(kvr, kvc), mean))
colnames(KG)=kt.name
barplot(as.matrix(KG), ylab= "Genetic varaince", beside=TRUE, col=rainbow(length(unique(Compression[,2]))))
KG<- t(tapply(as.numeric(Compression[,6]), list(kvr, kvc), mean))
colnames(KG)=kt.name
barplot(as.matrix(KG), ylab= "Residual varaince", beside=TRUE, col=rainbow(length(unique(Compression[,2]))))
KG<- t(tapply(as.numeric(Compression[,5])/(as.numeric(Compression[,5])+as.numeric(Compression[,6])), list(kvr, kvc), mean))
colnames(KG)=kt.name
barplot(as.matrix(KG), ylab= "Heritability", beside=TRUE, col=rainbow(length(unique(Compression[,2]))),ylim=c(0,1))
legend("topleft", paste(t(ca.name)), cex=0.8,bty="n", fill=rainbow(length(unique(Compression[,2]))),horiz=TRUE)
dev.off()
} #end of Graph compression with single groups
print("GAPIT.Compression.Visualization accomplished successfully!")
#return(list(compression=Compression.h2,h2=h2.opt))
return
}#GAPIT.Compression.Plots ends here
#=============================================================================================
`GAPIT.Create.Indicator` <-
function(xs, SNP.impute = "Major" ){
#Object: To esimate variance component by using EMMA algorithm and perform GWAS with P3D/EMMAx
#Output: ps, REMLs, stats, dfs, vgs, ves, BLUP, BLUP_Plus_Mean, PEV
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: April 30, 2012
##############################################################################################
#Determine the number of bits of the genotype
bit=nchar(as.character(xs[1]))
#Identify the SNPs classified as missing
if(bit==1) {
xss[xss=="xs"]="N"
xs[xs=="-"]="N"
xs[xs=="+"]="N"
xs[xs=="/"]="N"
xs[xs=="K"]="Z" #K (for GT genotype)is is replaced by Z to ensure heterozygose has the largest value
}
if(bit==2) {
xs[xs=="xsxs"]="N"
xs[xs=="--"]="N"
xs[xs=="++"]="N"
xs[xs=="//"]="N"
xs[xs=="NN"]="N"
}
#Create the indicators
#Sort the SNPs by genotype frequency
xs.temp <- xs[-which(xs == "N")]
frequ<- NULL
for(i in 1:length(unique(xs.temp))) frequ <- c(frequ, length(which(xs == unique(xs)[i])))
unique.sorted <- cbind(unique(xs.temp), frequ)
print("unique.sorted is")
print(unique.sorted)
unique.sorted <- unique.sorted[order(unique.sorted[,2]),]
unique.sorted <- unique.sorted[,-2]
#Impute based on the major and minor allele frequencies
if(SNP.impute == "Major") xs[which(is.na(xs))] = unique.sorted[1]
if(SNP.impute == "Minor") xs[which(is.na(xs))] = unique.sorted[length(unique.sorted)]
if(SNP.impute == "Middle") xs[which(is.na(xs))] = unique.sorted[2]
x.ind <- NULL
for(i in unique.sorted){
x.col <- rep(NA, length(xs))
x.col[which(xs==i)] <- 1
x.col[which(xs!=i)] <- 0
x.ind <- cbind(x.ind,x.col)
}
return(x.ind)
print("GAPIT.Create.Indicator accomplished successfully!")
}#end of GAPIT.Create.Indicator function
#=============================================================================================
`GAPIT.DP` <-
function(G=NULL,GD=NULL,GM=NULL,KI=NULL,Z=NULL,CV=NULL,CV.Inheritance=NULL,GP=NULL,GK=NULL,
group.from=30 ,group.to=1000000,group.by=10,DPP=100000,
kinship.cluster="average", kinship.group='Mean',kinship.algorithm="VanRaden",
bin.from=10000,bin.to=10000,bin.by=10000,inclosure.from=10,inclosure.to=10,inclosure.by=10,
SNP.P3D=TRUE,SNP.effect="Add",SNP.impute="Middle",PCA.total=0, SNP.fraction = 1, seed = 123, BINS = 20,SNP.test=TRUE,
SNP.MAF=0,FDR.Rate = 1, SNP.FDR=1,SNP.permutation=FALSE,SNP.CV=NULL,SNP.robust="GLM", NJtree.group=NULL,NJtree.type=c("fan","unrooted"),plot.bin=10^6,PCA.col=NULL,PCA.3d=FALSE,
file.from=1, file.to=1, file.total=NULL, file.fragment = 99999,file.path=NULL,Inter.Plot=FALSE,Inter.type=c("m","q"),
file.G=NULL, file.Ext.G=NULL,file.GD=NULL, file.GM=NULL, file.Ext.GD=NULL,file.Ext.GM=NULL,
ngrid = 100, llim = -10, ulim = 10, esp = 1e-10, Multi_iter=FALSE,windowsize=5e9,
LD.chromosome=NULL,LD.location=NULL,LD.range=NULL, p.threshold=NA,QTN.threshold=0.01,maf.threshold=0.03,
sangwich.top=NULL,sangwich.bottom=NULL,QC=TRUE,GTindex=NULL,LD=0.1,
file.output=TRUE,cutOff=0.01, Model.selection = FALSE,output.numerical = FALSE,
output.hapmap = FALSE, Create.indicator = FALSE,QTN=NULL, QTN.round=1,QTN.limit=0, QTN.update=TRUE, QTN.method="Penalty", Major.allele.zero = FALSE,
method.GLM="fast.lm",method.sub="reward",method.sub.final="reward",method.bin="static",bin.size=c(1000000),bin.selection=c(10,20,50,100,200,500,1000),
memo="",Prior=NULL,ncpus=1,maxLoop=3,threshold.output=.01, WS=c(1e0,1e3,1e4,1e5,1e6,1e7),alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),maxOut=100,QTN.position=NULL,
converge=1,iteration.output=FALSE,acceleration=0,iteration.method="accum",PCA.View.output=TRUE,Geno.View.output=TRUE,plot.style="Oceanic",SUPER_GD=NULL,SUPER_GS=FALSE,CG=NULL,model="MLM"){
#Object: To Data and Parameters
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("GAPIT.DP in process...")
#Judge phenotype genotype and GAPIT logical
#print(file.from)
#print(kinship.algorithm)
#print(NJtree.group)
myGenotype<-GAPIT.Genotype(G=G,GD=GD,GM=GM,KI=KI,PCA.total=PCA.total,kinship.algorithm=kinship.algorithm,SNP.fraction=SNP.fraction,SNP.test=FALSE,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,
file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF=SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,NJtree.group=NJtree.group,NJtree.type=NJtree.type,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,
GP=GP,GK=GK,bin.size=NULL,inclosure.size=NULL,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,GTindex=NULL,file.output=file.output, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero,Geno.View.output=Geno.View.output,PCA.col=PCA.col,PCA.3d=PCA.3d)
# }
KI=myGenotype$KI
PC=myGenotype$PC
print(dim(PC))
genoFormat=myGenotype$genoFormat
hasGenotype=myGenotype$hasGenotype
byFile=myGenotype$byFile
fullGD=myGenotype$fullGD
GD=myGenotype$GD
GI=myGenotype$GI
GT=myGenotype$GT
G=myGenotype$G
chor_taxa=myGenotype$chor_taxa
#if G exist turn to GD and GM
if(output.numerical) write.table(GD, "GAPIT.Genotype.Numerical.txt", quote = FALSE, sep = "\t", row.names = TRUE,col.names = NA)
if(output.hapmap) write.table(myGenotype$G, "GAPIT.Genotype.hmp.txt", quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
rownames(GD)=GT
colnames(GD)=GI[,1]
GD=cbind(as.data.frame(GT),GD)
print("GAPIT.DP accomplished successfully for multiple traits. Results are saved")
return (list(Y=NULL,G=G,GD=GD,GM=GI,KI=KI,Z=Z,CV=CV,CV.Inheritance= CV.Inheritance,GP=GP,GK=GK,PC=PC,GI=GI,
group.from= group.from ,group.to= group.to,group.by= group.by,DPP= DPP, name.of.trait=NULL,
kinship.cluster= kinship.cluster, kinship.group= kinship.group,kinship.algorithm= kinship.algorithm,NJtree.group=NJtree.group,NJtree.type=NJtree.type,PCA.col=PCA.col,PCA.3d=PCA.3d,
bin.from= bin.from,bin.to= bin.to,bin.by= bin.by,inclosure.from= inclosure.from,inclosure.to= inclosure.to,inclosure.by= inclosure.by,
SNP.P3D= SNP.P3D,SNP.effect= SNP.effect,SNP.impute= SNP.impute,PCA.total= PCA.total, SNP.fraction = SNP.fraction, seed = seed,
BINS = BINS,SNP.test=SNP.test, SNP.MAF= SNP.MAF,FDR.Rate = FDR.Rate, SNP.FDR= SNP.FDR,SNP.permutation= SNP.permutation,
SNP.CV= SNP.CV,SNP.robust= SNP.robust, file.from= file.from, file.to=file.to, file.total= file.total, file.fragment = file.fragment,file.path= file.path,
file.G= file.G, file.Ext.G= file.Ext.G,file.GD= file.GD, file.GM= file.GM, file.Ext.GD= file.Ext.GD,file.Ext.GM= file.Ext.GM,
ngrid = ngrid, llim = llim, ulim = ulim, esp = esp,Inter.Plot=Inter.Plot,Inter.type=Inter.type,
LD.chromosome= LD.chromosome,LD.location= LD.location,LD.range= LD.range,Multi_iter=Multi_iter,
sangwich.top= sangwich.top,sangwich.bottom= sangwich.bottom,QC= QC,GTindex= GTindex,LD= LD,GT=GT,
file.output= file.output,cutOff=cutOff, Model.selection = Model.selection,output.numerical = output.numerical,
output.hapmap = output.hapmap, Create.indicator = Create.indicator,
QTN= QTN, QTN.round= QTN.round,QTN.limit= QTN.limit, QTN.update= QTN.update, QTN.method= QTN.method, Major.allele.zero = Major.allele.zero,
method.GLM= method.GLM,method.sub= method.sub,method.sub.final= method.sub.final,
method.bin= method.bin,bin.size= bin.size,bin.selection= bin.selection,
memo= memo,Prior= Prior,ncpus=1,maxLoop= maxLoop,threshold.output= threshold.output,
WS= WS,alpha= alpha,maxOut= maxOut,QTN.position= QTN.position, converge=1,iteration.output= iteration.output,acceleration=0,
iteration.method= iteration.method,PCA.View.output= PCA.View.output,
p.threshold=p.threshold,QTN.threshold=QTN.threshold,
maf.threshold=maf.threshold,chor_taxa=chor_taxa,windowsize=windowsize,
Geno.View.output= Geno.View.output,plot.style= plot.style,SUPER_GD= SUPER_GD,SUPER_GS= SUPER_GS,CG=CG,plot.bin=plot.bin))
} #end of GAPIT DP function
#=============================================================================================
`GAPIT.EMMAxP3D` <-
function(ys,xs,K=NULL,Z=NULL,X0=NULL,CVI=NULL,CV.Inheritance=NULL,GI=NULL,GP=NULL,
file.path=NULL,file.from=NULL,file.to=NULL,file.total=1, genoFormat="Hapmap", file.fragment=NULL,byFile=FALSE,fullGD=TRUE,SNP.fraction=1,
file.G=NULL,file.Ext.G=NULL,GTindex=NULL,file.GD=NULL, file.GM=NULL, file.Ext.GD=NULL,file.Ext.GM=NULL,
SNP.P3D=TRUE,Timmer,Memory,optOnly=TRUE,SNP.effect="Add",SNP.impute="Middle", SNP.permutation=FALSE,
ngrids=100,llim=-10,ulim=10,esp=1e-10,name.of.trait=NULL, Create.indicator = FALSE, Major.allele.zero = FALSE){
#Object: To esimate variance component by using EMMA algorithm and perform GWAS with P3D/EMMAx
#Output: ps, REMLs, stats, dfs, vgs, ves, BLUP, BLUP_Plus_Mean, PEV
#Authors: Feng Tian, Alex Lipka and Zhiwu Zhang
# Last update: April 6, 2016
# Library used: EMMA (Kang et al, Genetics, Vol. 178, 1709-1723, March 2008)
# Note: This function was modified from the function of emma.REML.t from the library
##############################################################################################
#print("EMMAxP3D started...")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="P3D Start")
Memory=GAPIT.Memory(Memory=Memory,Infor="P3D Start")
#When numeric genotypes are selected, impute the missing SNPs with the allele indicated by the "SNP.impute" value
if(!optOnly){
if(SNP.impute == "Major") xs[which(is.na(xs))] = 2
if(SNP.impute == "Minor") xs[which(is.na(xs))] = 0
if(SNP.impute == "Middle") xs[which(is.na(xs))] = 1
}
#--------------------------------------------------------------------------------------------------------------------<
#Change data to matrix format if they are not
if(is.null(dim(ys)) || ncol(ys) == 1) ys <- matrix(ys, 1, length(ys))
if(is.null(X0)) X0 <- matrix(1, ncol(ys), 1)
#handler of special Z and K
if(!is.null(Z)){ if(ncol(Z) == nrow(Z)) Z = NULL }
if(!is.null(K)) {if(length(K)<= 1) K = NULL}
#Extract dimension information
g <- nrow(ys) #number of traits
n <- ncol(ys) #number of observation
q0 <- ncol(X0)#number of fixed effects
q1 <- q0 + 1 #Nuber of fixed effect including SNP
nr=n
if(!is.null(K)) tv=ncol(K)
#decomposation without fixed effect
#print("Caling emma.eigen.L...")
if(!is.null(K)) eig.L <- emma.eigen.L(Z, K) #this function handle both NULL Z and non-NULL Z matrix
#eig.L$values[eig.L$values<0]=0
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="eig.L")
Memory=GAPIT.Memory(Memory=Memory,Infor="eig.L")
#decomposation with fixed effect (SNP not included)
#print("Calling emma.eigen.R.w.Z...")
X <- X0 #covariate variables such as population structure
if(!is.null(Z) & !is.null(K)) eig.R <- try(emma.eigen.R.w.Z(Z, K, X),silent=TRUE) #This will be used to get REstricted ML (REML)
if(is.null(Z) & !is.null(K)) eig.R <- try(emma.eigen.R.wo.Z( K, X),silent=TRUE) #This will be used to get REstricted ML (REML)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="eig.R")
Memory=GAPIT.Memory(Memory=Memory,Infor="eig.R")
#eig.R$values[eig.R$values<0]=0
#print(labels(eig.R))
#print(length(eig.R$values))
#print(dim(eig.R$vectors))
#print("emma.eigen.R.w.Z called!!!")
#Handler of error in emma
#print("!!!!!!")
if(!is.null(K)){
if(inherits(eig.R, "try-error"))
return(list(ps = NULL, REMLs = NA, stats = NULL, effect.est = NULL, dfs = NULL,maf=NULL,nobs = NULL,Timmer=Timmer,Memory=Memory,
vgs = NA, ves = NA, BLUP = NULL, BLUP_Plus_Mean = NULL,
PEV = NULL, BLUE=NULL))
#print("@@@@@")
}
#-------------------------------------------------------------------------------------------------------------------->
#print("Looping through traits...")
#Loop on Traits
for (j in 1:g)
{
if(optOnly){
#REMLE <- GAPIT.emma.REMLE(ys[j,], X, K, Z, ngrids, llim, ulim, esp, eig.R)
#vgs <- REMLE$vg
#ves <- REMLE$ve
#REMLs <- REMLE$REML
#REMLE_delta=REMLE$delta
if(!is.null(K)){
REMLE <- GAPIT.emma.REMLE(ys[j,], X, K, Z, ngrids, llim, ulim, esp, eig.R)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="REML")
Memory=GAPIT.Memory(Memory=Memory,Infor="REML")
rm(eig.R)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="eig.R removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="eig.R removed")
vgs <- REMLE$vg
ves <- REMLE$ve
REMLs <- REMLE$REML
REMLE_delta=REMLE$delta
rm(REMLE)
gc()
}
vids <- !is.na(ys[j,])
yv <- ys[j, vids]
if(!is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix(c(sqrt(1/(eig.L$values + REMLE_delta)),rep(sqrt(1/REMLE_delta),nr - tv)),nr,((nr-tv)+length(eig.L$values)),byrow=TRUE)
if( is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix( sqrt(1/(eig.L$values + REMLE_delta)),nr,length(eig.L$values),byrow=TRUE)
if( !is.null(Z) & !is.null(K)) eig.full.plus.delta <- as.matrix(c((eig.L$values + REMLE_delta), rep(REMLE_delta,(nr - tv))))
if( is.null(Z) & !is.null(K)) eig.full.plus.delta <- as.matrix((eig.L$values + REMLE_delta))
if(!is.null(K)){
if(length(which(eig.L$values < 0)) > 0 ){
#print("---------------------------------------------------The group kinship matrix at this compression level is not positive semidefinite. Please select another compression level.---------------------------------------------------")
#return(list(ps = NULL, REMLs = 999999, stats = NULL, effect.est = NULL, dfs = NULL,maf=NULL,nobs = NULL,Timmer=Timmer,Memory=Memory,
#vgs = 1.000, ves = 1.000, BLUP = NULL, BLUP_Plus_Mean = NULL,
#PEV = NULL, BLUE=NULL))
}
}
#Calculate the log likelihood function for the intercept only model
X.int <- matrix(1,nrow(as.matrix(yv)),ncol(as.matrix(yv)))
iX.intX.int <- solve(crossprod(X.int, X.int))
iX.intY <- crossprod(X.int, as.matrix(as.matrix(yv)))
beta.int <- crossprod(iX.intX.int, iX.intY) #Note: we can use crossprod here becase iXX is symmetric
X.int.beta.int <- X.int%*%beta.int
logL0 <- 0.5*((-length(yv))*log(((2*pi)/length(yv))
*crossprod((yv-X.int.beta.int),(yv-X.int.beta.int)))
-length(yv))
#print(paste("The value of logL0 inside of the optonly template is is",logL0, sep = ""))
#print(paste("The value of nrow(as.matrix(ys[!is.na(ys)])) is ",nrow(as.matrix(ys[!is.na(ys)])), sep = ""))
if(!is.null(K)){
yt <- yt <- crossprod(U, yv)
X0t <- crossprod(U, X0)
X0X0 <- crossprod(X0t, X0t)
X0Y <- crossprod(X0t,yt)
XY <- X0Y
iX0X0 <- try(solve(X0X0),silent=TRUE)
if(inherits(iX0X0, "try-error")){
iX0X0 <- ginv(X0X0)
print("At least two of your covariates are linearly dependent. Please reconsider the covariates you are using for GWAS and GPS")
}
iXX <- iX0X0
}
if(is.null(K)){
iXX <- try(solve(crossprod(X,X)),silent=TRUE)
if(inherits(iXX, "try-error"))iXX <- ginv(crossprod(X,X))
XY = crossprod(X,yv)
}
beta <- crossprod(iXX,XY) #Note: we can use crossprod here because iXX is symmetric
X.beta <- X%*%beta
beta.cv=beta
BLUE=X.beta
if(!is.null(K)){
U.times.yv.minus.X.beta <- crossprod(U,(yv-X.beta))
logLM <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta))
- sum(log(eig.full.plus.delta)) - length(yv))
}
if(is.null(K)){
U.times.yv.minus.X.beta <- yv-X.beta
logLM <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta)) - length(yv))
}
}#End if(optOnly)
#--------------------------------------------------------------------------------------------------------------------<
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Trait")
Memory=GAPIT.Memory(Memory=Memory,Infor="Trait")
if(!is.null(K)){
REMLE <- GAPIT.emma.REMLE(ys[j,], X, K, Z, ngrids, llim, ulim, esp, eig.R)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="REML")
Memory=GAPIT.Memory(Memory=Memory,Infor="REML")
rm(eig.R)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="eig.R removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="eig.R removed")
vgs <- REMLE$vg
ves <- REMLE$ve
REMLs <- REMLE$REML
REMLE_delta=REMLE$delta
rm(REMLE)
gc()
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="REMLE removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="REMLE removed")
if(!is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix(c(sqrt(1/(eig.L$values + REMLE_delta)),rep(sqrt(1/REMLE_delta),nr - tv)),nr,((nr-tv)+length(eig.L$values)),byrow=TRUE)
if( is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix( sqrt(1/(eig.L$values + REMLE_delta)),nr,length(eig.L$values),byrow=TRUE)
if( !is.null(Z) & !is.null(K)) eig.full.plus.delta <- as.matrix(c((eig.L$values + REMLE_delta), rep(REMLE_delta,(nr - tv))))
if( is.null(Z) & !is.null(K)) eig.full.plus.delta <- as.matrix((eig.L$values + REMLE_delta))
if(!is.null(K)){
if(length(which(eig.L$values < 0)) > 0 ){
#print("---------------------------------------------------The group kinship matrix at this compression level is not positive semidefinite. Please select another compression level.---------------------------------------------------")
#return(list(ps = NULL, REMLs = 999999, stats = NULL, effect.est = NULL, dfs = NULL,maf=NULL,nobs = NULL,Timmer=Timmer,Memory=Memory,
#vgs = 1.000, ves = 1.000, BLUP = NULL, BLUP_Plus_Mean = NULL,
#PEV = NULL, BLUE=NULL))
}
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="U Matrix")
Memory=GAPIT.Memory(Memory=Memory,Infor="U Matrix")
if(SNP.P3D == TRUE)rm(eig.L)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="eig.L removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="eig.L removed")
#-------------------------------------------------------------------------------------------------------------------->
#The cases that go though multiple file once
file.stop=file.to
if(optOnly) file.stop=file.from
if(fullGD) file.stop=file.from
if(!fullGD & !optOnly) {print("Screening SNPs from file...")}
#Add loop for genotype data files
for (file in file.from:file.stop)
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="New Genotype file")
Memory=GAPIT.Memory(Memory=Memory,Infor="New Genotype file")
frag=1
numSNP=file.fragment
myFRG=NULL
while(numSNP==file.fragment) { #this is problematic if the read end at the last line
#initial previous SNP storage
x.prev <- vector(length = 0)
#force to skip the while loop if optOnly
if(optOnly) numSNP=0
#Determine the case of first file and first fragment: skip read file
if(file==file.from & frag==1& SNP.fraction<1){
firstFileFirstFrag=TRUE
}else{
firstFileFirstFrag=FALSE
}
#In case of xs is not full GD, replace xs from file
if(!fullGD & !optOnly & !firstFileFirstFrag )
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Clean myFRG")
Memory=GAPIT.Memory(Memory=Memory,Infor="Clean myFRG")
#update xs for each file
rm(xs)
rm(myFRG)
gc()
print(paste("Current file: ",file," , Fragment: ",frag,sep=""))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Read file fragment")
Memory=GAPIT.Memory(Memory=Memory,Infor="Read file fragment")
myFRG=GAPIT.Fragment( file.path=file.path, file.total=file.total,file.G=file.G,file.Ext.G=file.Ext.G,
seed=seed,SNP.fraction=SNP.fraction,SNP.effect=SNP.effect,SNP.impute=SNP.impute,genoFormat=genoFormat,
file.GD=file.GD,file.Ext.GD=file.Ext.GD,file.GM=file.GM,file.Ext.GM=file.Ext.GM,file.fragment=file.fragment,file=file,frag=frag,
Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype file converted")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype file converted")
#print("-----------------------------------------------------------------")
if(is.null(myFRG$GD)){
xs=NULL
}else{
xs=myFRG$GD[GTindex,]
}
if(!is.null(myFRG$GI)) {
colnames(myFRG$GI)=c("SNP","Chromosome","Position")
GI=as.matrix(myFRG$GI)
}
if(!is.null(myFRG$GI)) {
numSNP=ncol(myFRG$GD)
} else{
numSNP=0
}
if(is.null(myFRG))numSNP=0 #force to end the while loop
} # end of if(!fullGD)
if(fullGD)numSNP=0 #force to end the while loop
#Skip REML if xs is from a empty fragment file
if(!is.null(xs)) {
if(is.null(dim(xs)) || nrow(xs) == 1) xs <- matrix(xs, length(xs),1)
xs <- as.matrix(xs)
if(length(which(is.na(xs)))>0){ #for the case where fragments are read in
if(SNP.impute == "Major") xs[which(is.na(xs))] = 2
if(SNP.impute == "Minor") xs[which(is.na(xs))] = 0
if(SNP.impute == "Middle") xs[which(is.na(xs))] = 1
}
m <- ncol(xs) #number of SNPs
t <- nrow(xs) #number of individuals
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before cleaning")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before cleaning")
#allocate spaces for SNPs
rm(dfs)
rm(stats)
rm(effect.est)
rm(ps)
rm(nobs)
rm(maf)
rm(rsquare_base)
rm(rsquare)
rm(df)
rm(tvalue)
rm(stderr)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="After cleaning")
Memory=GAPIT.Memory(Memory=Memory,Infor="After cleaning")
dfs <- matrix(nrow = m, ncol = g)
stats <- matrix(nrow = m, ncol = g)
if(!Create.indicator) effect.est <- matrix(nrow = m, ncol = g)
if(Create.indicator) effect.est <- NULL
ps <- matrix(nrow = m, ncol = g)
nobs <- matrix(nrow = m, ncol = g)
maf <- matrix(nrow = m, ncol = g)
rsquare_base <- matrix(nrow = m, ncol = g)
rsquare <- matrix(nrow = m, ncol = g)
df <- matrix(nrow = m, ncol = g)
tvalue <- matrix(nrow = m, ncol = g)
stderr <- matrix(nrow = m, ncol = g)
#print(paste("Memory allocated.",sep=""))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Memory allocation")
Memory=GAPIT.Memory(Memory=Memory,Infor="Memory allocation")
if(optOnly)mloop=0
if(!optOnly)mloop=m
#Loop on SNPs
#print(paste("Number of SNPs is ",mloop," in genotype file ",file, sep=""))
#set starting point of loop
if(file==file.from&frag==1){loopStart=0}else{loopStart=1}
for (i in loopStart:mloop){
#print(i)
#--------------------------------------------------------------------------------------------------------------------<
normalCase=TRUE
if((i >0)&(floor(i/1000)==i/1000)) {print(paste("Genotype file: ", file,", SNP: ",i," ",sep=""))}
# To extract current snp. It save computation for next one in case they are identical
if(i ==0&file==file.from&frag==1){
#For the model without fitting SNP
vids <- !is.na(ys[j,]) #### Feng changed
xv <- ys[j, vids]*0+1 #### Feng changed
}
if(i >0 | file>file.from | frag>1){
if(Create.indicator){ #I need create indicators and then calculate the minor allele frequency
condition.temp <- unique(xs[vids,i])
#Define what a bit is
bit=nchar(as.character(xs[vids[1],i]))
#Expand on the "which" statement below to include all instances of missing data
if(bit==1) condition <- condition.temp[-which(condition.temp == "N")]
if(bit==2) condition <- condition.temp[-which(condition.temp == "NN")]
#print("condition.temp is ")
#print(condition.temp)
#print("condition is")
#print(condition)
#print(paste("The value of i is ", i, sep = ""))
if(length(condition) <= 1){
dfs[i, ] <- rep(NA, g)
stats[i, ] <- rep(NA, g)
effect.est <- rbind(effect.est, c(i,rep(NA, g), rep(NA, g)))
ps[i, ] = rep(1, g)
rsquare[i, ] <- rep(NA,g)
rsquare_base[i, ]<-rep(NA,g)
maf[i, ] <- rep(0, g)
df[i, ] <- rep(NA,g)
tvalue[i, ] <- rep(NA,g)
stderr[i, ] <- rep(NA,g)
normalCase=FALSE
x.prev= vector(length = 0)
}
}
if(normalCase){
#print("The head of xs[vids,i] is")
#print(head(xs[vids,i]))
if(Create.indicator){ #I need create indicators and then calculate the minor allele frequency
indicator <- GAPIT.Create.Indicator(xs[vids,i], SNP.impute = SNP.impute)
xv <- indicator$x.ind
vids <- !is.na(xv[,1]) #### Feng changed
vids.TRUE=which(vids==TRUE)
vids.FALSE=which(vids==FALSE)
ns=nrow(xv)
ss=sum(xv[,ncol(xv)])
maf[i]=min(ss/ns,1-ss/ns)
nobs[i]=ns
q1 <- q0 + ncol(xv) # This is done so that parameter estimates for all indicator variables are included
#These two matrices need to be reinitiated for each SNP.
Xt <- matrix(NA,nr, q1)
iXX=matrix(NA,q1,q1)
}
}
if(!Create.indicator){ #### Feng changed
#print(xs[1:10,1:10])
xv <- xs[vids,i]
vids <- !is.na(xs[,i]) #### Feng changed
vids.TRUE=which(vids==TRUE)
vids.FALSE=which(vids==FALSE)
ns=length(xv)
#print(xv))
ss=sum(xv)
maf[i]=min(.5*ss/ns,1-.5*ss/ns)
nobs[i]=ns
}
nr <- sum(vids)
if(i ==1 & file==file.from&frag==1 & !Create.indicator) {
Xt <- matrix(NA,nr, q1)
iXX=matrix(NA,q1,q1)
}
}
#Situation of no variation for SNP except the fisrt one(synthetic for EMMAx/P3D)
if((min(xv) == max(xv)) & (i >0 | file>file.from |frag>1))
{
dfs[i, ] <- rep(NA, g)
stats[i, ] <- rep(NA, g)
if(!Create.indicator) effect.est[i,] <- rep(NA, g)
if(Create.indicator) effect.est <- rbind(effect.est, c(i,rep(NA, g),rep(NA, g)))
ps[i, ] = rep(1, g)
rsquare[i, ] <- rep(NA,g)
rsquare_base[i, ]<-rep(NA,g)
df[i, ] <- rep(NA,g)
tvalue[i, ] <- rep(NA,g)
stderr[i, ] <- rep(NA,g)
normalCase=FALSE
}else if(identical(x.prev, xv)) #Situation of the SNP is identical to previous
{
if(i >1 | file>file.from | frag>1){
dfs[i, ] <- dfs[i - 1, ]
stats[i, ] <- stats[i - 1, ]
if(!Create.indicator) effect.est[i, ] <- effect.est[i - 1, ]
if(Create.indicator) effect.est <- rbind(effect.est, c(i, rep(NA, g), rep(NA, g))) #If the previous SNP is idnetical, indicate this by "NA"
ps[i, ] <- ps[i - 1, ]
rsquare[i, ] <- rsquare[i - 1, ]
rsquare_base[i, ] <-rsquare_base[i - 1, ]
df[i, ] <- df[i - 1, ]
tvalue[i, ] <- tvalue[i - 1, ]
stderr[i, ] <- stderr[i - 1, ]
normalCase=FALSE
}
}
#-------------------------------------------------------------------------------------------------------------------->
if(i == 0 &file==file.from &frag==1){
#Calculate the log likelihood function for the intercept only model
#vids <- !is.na(ys[j,])
yv <- ys[j, vids]
X.int <- matrix(1,nrow(as.matrix(yv)),ncol(as.matrix(yv)))
iX.intX.int <- solve(crossprod(X.int, X.int))
iX.intY <- crossprod(X.int, as.matrix(as.matrix(yv)))
beta.int <- crossprod(iX.intX.int, iX.intY) #Note: we can use crossprod here becase iXX is symmetric
X.int.beta.int <- X.int%*%beta.int
#X.int <- matrix(1,nrow(as.matrix(ys[!is.na(ys)])),ncol(as.matrix(ys[!is.na(ys)])))
#iX.intX.int <- solve(crossprod(X.int, X.int))
#iX.intY <- crossprod(X.int, as.matrix(ys[!is.na(ys)]))
#beta.int <- crossprod(iX.intX.int, iX.intY) #Note: we can use crossprod here becase iXX is symmetric
#X.int.beta.int <- X.int%*%beta.int
logL0 <- 0.5*((-length(yv))*log(((2*pi)/length(yv))
*crossprod((yv-X.int.beta.int),(yv-X.int.beta.int)))
-length(yv))
#logL0 <- 0.5*((-nrow(as.matrix(ys[!is.na(ys)])))*log(((2*pi)/nrow(ys))
# *crossprod(((as.matrix(ys[!is.na(ys)]))-X.int.beta.int),((as.matrix(ys[!is.na(ys)]))-X.int.beta.int)))
# -nrow(as.matrix(ys[!is.na(ys)])))
#print(paste("The value of logL0 inside of the calculating SNPs loop is", logL0, sep = ""))
}
#Normal case
if(normalCase)
{
#--------------------------------------------------------------------------------------------------------------------<
#nv <- sum(vids)
yv <- ys[j, vids] #### Feng changed
nr <- sum(vids) #### Feng changed
if(!is.null(Z) & !is.null(K))
{
r<- ncol(Z) ####Feng, add a variable to indicate the number of random effect
vran <- vids[1:r] ###Feng, add a variable to indicate random effects with nonmissing genotype
tv <- sum(vran) #### Feng changed
}
#-------------------------------------------------------------------------------------------------------------------->
#--------------------------------------------------------------------------------------------------------------------<
if(i >0 | file>file.from|frag>1) dfs[i, j] <- nr - q1
if(i >0 | file>file.from|frag>1){
if(!Create.indicator) X <- cbind(X0[vids, , drop = FALSE], xs[vids,i])
if(Create.indicator){
X <- cbind(X0[vids, , drop = FALSE], xv)
#if(i == 1) {print("the head of X for running GWAS is")}
#if(i == 1) {print(head(X))}
}
}
#Recalculate eig and REML if not using P3D NOTE THIS USED TO BE BEFORE the two solid lines
if(SNP.P3D==FALSE & !is.null(K))
{
if(!is.null(Z)) eig.R <- emma.eigen.R.w.Z(Z, K, X) #This will be used to get REstricted ML (REML)
if(is.null(Z)) eig.R <- emma.eigen.R.wo.Z( K, X) #This will be used to get REstricted ML (REML)
if(!is.null(Z)) REMLE <- GAPIT.emma.REMLE(ys[j,], X, K, Z, ngrids, llim, ulim, esp, eig.R)
if(is.null(Z)) REMLE <- GAPIT.emma.REMLE(ys[j,], X, K, Z = NULL, ngrids, llim, ulim, esp, eig.R)
if(!is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix(c(sqrt(1/(eig.L$values + REMLE$delta)),rep(sqrt(1/REMLE$delta),nr - tv)),nr,((nr-tv)+length(eig.L$values)),byrow=TRUE)
if(is.null(Z) & !is.null(K)) U <- eig.L$vectors * matrix( sqrt(1/(eig.L$values + REMLE$delta)),nr,length(eig.L$values),byrow=TRUE)
vgs <- REMLE$vg
ves <- REMLE$ve
REMLs <- REMLE$REML
REMLE_delta=REMLE$delta
}
if(n==nr)
{
if(!is.null(K))
{
yt <- crossprod(U, yv)
if(i == 0 &file==file.from &frag==1){
X0t <- crossprod(U, X0)
Xt <- X0t
}
if(i > 0 | file>file.from |frag>1){
#if(i ==1 & file==file.from&frag==1) Xt <- matrix(NA,nr, q1)
if(Create.indicator){
xst <- crossprod(U, X[,(q0+1):q1])
Xt[1:nr,1:q0] <- X0t
Xt[1:nr,(q0+1):q1] <- xst
}
#print(paste("i:",i,"q0:",q0,"q1:",q1,"nt:",nr,"XT row",nrow(Xt),"XT col",ncol(Xt),sep=" "))
if(!Create.indicator){
xst <- crossprod(U, X[,ncol(X)])
Xt[1:nr,1:q0] <- X0t
Xt[1:nr,q1] <- xst
}
}
}else{
yt=yv
if(i == 0 &file==file.from &frag==1) X0t <- X0
if(i > 0 | file>file.from |frag>1) xst <- X[,ncol(X)]
}
if(i == 0 &file==file.from &frag==1){
X0X0 <- crossprod(X0t, X0t)
#XX <- X0X0
}
if(i > 0 | file>file.from |frag>1){
#if(i == 1)XX=matrix(NA,q1,q1)
X0Xst <- crossprod(X0t,xst)
XstX0 <- t(X0Xst)
xstxst <- crossprod(xst, xst)
# if(i == 1){
# Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Calculate_X0Xst_XstX0_xstxst")
# Memory=GAPIT.Memory(Memory=Memory,Infor="Calculate_X0Xst_XstX0_xstxst")
# }
#XX <- rbind(cbind(X0X0, X0Xst), cbind(XstX0, xstxst))
#XX[1:q0,1:q0] <- X0X0
#XX[q1,1:q0] <- X0Xst
#XX[1:q0,q1] <- X0Xst
#XX[q1,q1] <- xstxst
}
if(X0X0[1,1] == "NaN")
{
Xt[which(Xt=="NaN")]=0
yt[which(yt=="NaN")]=0
XX=crossprod(Xt, Xt)
}
if(i == 0 &file==file.from & frag==1){
X0Y <- crossprod(X0t,yt)
XY <- X0Y
}
if(i > 0 | file>file.from |frag>1){
xsY <- crossprod(xst,yt)
XY <- c(X0Y,xsY)
# if(i == 1){
# Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Calculate_xsY_X0Y")
# Memory=GAPIT.Memory(Memory=Memory,Infor="Calculate_xsY_X0Y")
# }
}
#XY = crossprod(Xt,yt)
}
#Missing SNP
if(n>nr)
{
UU=crossprod(U,U)
A11=UU[vids.TRUE,vids.TRUE]
A12=UU[vids.TRUE,vids.FALSE]
A21=UU[vids.FALSE,vids.TRUE]
A22=UU[vids.FALSE,vids.FALSE]
A22i =try(solve(A22),silent=TRUE )
if(inherits(A22i, "try-error")) A22i <- ginv(A22)
F11=A11-A12%*%A22i%*%A21
XX=crossprod(X,F11)%*%X
XY=crossprod(X,F11)%*%yv
}
if(i == 0 &file==file.from &frag==1){
iX0X0 <- try(solve(X0X0),silent=TRUE)
if(inherits(iX0X0, "try-error")){
iX0X0 <- ginv(X0X0)
print("At least two of your covariates are linearly dependent. Please reconsider the covariates you are using for GWAS and GPS")
}
iXX <- iX0X0
}
if(i > 0 | file>file.from |frag>1){
#if(i ==1 &file==file.from &frag==1) iXX=matrix(NA,q1,q1)
if(Create.indicator){
B22 <- xstxst - XstX0%*%iX0X0%*%X0Xst
invB22 <- solve(B22)
B21 <- tcrossprod(XstX0, iX0X0)
NeginvB22B21 <- crossprod(-invB22,B21)
B11 <- iX0X0 + as.numeric(invB22)*crossprod(B21,B21)
iXX[1:q0,1:q0]=B11
iXX[(q0+1):q1,(q0+1):q1]=solve(B22)
iXX[(q0+1):q1,1:q0]=NeginvB22B21
iXX[1:q0,(q0+1):q1]=t(NeginvB22B21)
}
if(!Create.indicator){
B22 <- xstxst - XstX0%*%iX0X0%*%X0Xst
invB22 <- 1/B22
#B12 <- crossprod(iX0X0,X0Xst)
B21 <- tcrossprod(XstX0, iX0X0)
NeginvB22B21 <- crossprod(-invB22,B21)
#B11 <- iX0X0 + B12%*%invB22%*%B21
B11 <- iX0X0 + as.numeric(invB22)*crossprod(B21,B21)
#iXX <- rbind(cbind(B11,t(NeginvB22B21)), cbind(NeginvB22B21,invB22))
iXX[1:q0,1:q0]=B11
iXX[q1,q1]=1/B22
iXX[q1,1:q0]=NeginvB22B21
iXX[1:q0,q1]=NeginvB22B21
}
#if(i == 1){
# Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Calculate_iXX")
# Memory=GAPIT.Memory(Memory=Memory,Infor="Calculate_iXX")
#}
}
if(is.null(K)){
iXX <- try(solve(crossprod(X,X)),silent=TRUE)
if(inherits(iXX, "try-error"))iXX <- ginv(crossprod(X,X))
XY = crossprod(X,yv)
}
#iXX <- try(solve(XX))
#if(inherits(iXX, "try-error")) iXX <- ginv(crossprod(Xt, Xt))
#print("The dimension if iXX is")
#print(dim(iXX))
#print("The length of XY is")
#print(length(XY))
beta <- crossprod(iXX,XY) #Note: we can use crossprod here becase iXX is symmetric
#print("beta was estimated")
#-------------------------------------------------------------------------------------------------------------------->
#--------------------------------------------------------------------------------------------------------------------<
if(i ==0 &file==file.from &frag==1 & !is.null(K))
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="ReducedModel")
Memory=GAPIT.Memory(Memory=Memory,Infor="ReducdModel")
#beta.cv=beta
XtimesBetaHat <- X%*%beta
YminusXtimesBetaHat <- ys[j,]- XtimesBetaHat
vgK <- vgs*K
Dt <- crossprod(U, YminusXtimesBetaHat)
if(!is.null(Z)) Zt <- crossprod(U, Z)
if(is.null(Z)) Zt <- t(U)
if(X0X0[1,1] == "NaN")
{
Dt[which(Dt=="NaN")]=0
Zt[which(Zt=="NaN")]=0
}
BLUP <- K %*% crossprod(Zt, Dt) #Using K instead of vgK because using H=V/Vg
#print("!!!!")
#Clean up the BLUP starf to save memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="before Dt clean")
Memory=GAPIT.Memory(Memory=Memory,Infor="before Dt clean")
rm(Dt)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Dt clean")
Memory=GAPIT.Memory(Memory=Memory,Infor="Dt clean")
grand.mean.vector <- rep(beta[1], length(BLUP))
BLUP_Plus_Mean <- grand.mean.vector + BLUP
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="BLUP")
Memory=GAPIT.Memory(Memory=Memory,Infor="BLUP")
#PEV
C11=try(vgs*solve(crossprod(Xt,Xt)),silent=TRUE)
if(inherits(C11, "try-error")) C11=vgs*ginv(crossprod(Xt,Xt))
C21=-K%*%crossprod(Zt,Xt)%*%C11
Kinv=try(solve(K) ,silent=TRUE )
if(inherits(Kinv, "try-error")) Kinv=ginv(K)
if(!is.null(Z)) term.0=crossprod(Z,Z)/ves
if(is.null(Z)) term.0=diag(1/ves,nrow(K))
term.1=try(solve(term.0+Kinv/vgs ) ,silent=TRUE )
if(inherits(term.1, "try-error")) term.1=ginv(term.0+Kinv/vgs )
term.2=C21%*%crossprod(Xt,Zt)%*%K
C22=(term.1-term.2 )
PEV=as.matrix(diag(C22))
#print(paste("The value of is.na(CVI) is", is.na(CVI), sep = ""))
if(!is.na(CVI)){
XCV=as.matrix(cbind(1,data.frame(CVI[,-1])))
#CV.Inheritance specified
beta.Inheritance=beta
if(!is.null(CV.Inheritance)){
XCV=XCV[,1:(1+CV.Inheritance)]
beta.Inheritance=beta[1:(1+CV.Inheritance)]
}
#Interception only
if(length(beta)==1)XCV=X
BLUE=try(XCV%*%beta.Inheritance,silent=TRUE)
if(inherits(BLUE, "try-error")) BLUE = NA
#print("GAPIT just after BLUE")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PEV")
Memory=GAPIT.Memory(Memory=Memory,Infor="PEV")
}#end of if(i ==0&file==file.from & !is.null(K))
if(is.na(CVI)) BLUE = NA
}#end if(!is.na(CVI))
#-------------------------------------------------------------------------------------------------------------------->
#--------------------------------------------------------------------------------------------------------------------<
if(i ==0 &file==file.from &frag==1 & is.null(K))
{
YY=crossprod(yt, yt)
ves=(YY-crossprod(beta,XY))/(n-q0)
r=yt-X%*%iXX%*%XY
REMLs=-.5*(n-q0)*log(det(ves)) -.5*n -.5*(n-q0)*log(2*pi)
# REMLs=-.5*n*log(det(ves)) -.5*log(det(iXX)/ves) -.5*crossprod(r,r)/ves -.5*(n-q0)*log(2*pi)
vgs = 0
BLUP = 0
BLUP_Plus_Mean = NaN
PEV = ves
#print(paste("X row:",nrow(X)," col:",ncol(X)," beta:",length(beta),sep=""))
XCV=as.matrix(cbind(1,data.frame(CVI[,-1])))
#CV.Inheritance specified
beta.Inheritance=beta
if(!is.null(CV.Inheritance)){
XCV=XCV[,1:(1+CV.Inheritance)]
beta.Inheritance=beta[1:(1+CV.Inheritance)]
}
#Interception only
if(length(beta)==1)XCV=X
#BLUE=XCV%*%beta.Inheritance modified by jiabo wang 2016.11.21
BLUE=try(XCV%*%beta.Inheritance,silent=TRUE)
if(inherits(BLUE, "try-error")) BLUE = NA
}
#Clean up the BLUP stuff to save memory
if(i ==0 &file==file.from &frag==1 & !is.null(K))
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="K normal")
Memory=GAPIT.Memory(Memory=Memory,Infor="K normal")
if(SNP.P3D == TRUE) K=1 #NOTE: When SNP.P3D == FALSE, this line will mess up the spectral decomposition of the kinship matrix at each SNP.
rm(Dt)
rm(Zt)
rm(Kinv)
rm(C11)
rm(C21)
rm(C22)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="K set to 1")
Memory=GAPIT.Memory(Memory=Memory,Infor="K set to 1")
}
if(i == 0 &file==file.from & frag==1){
beta.cv=beta
X.beta <- X%*%beta
if(!is.null(K)){
U.times.yv.minus.X.beta <- crossprod(U,(yv-X.beta))
logLM_Base <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta))
- sum(log(eig.full.plus.delta)) - length(yv))
}
if(is.null(K)){
U.times.yv.minus.X.beta <- yv-X.beta
logLM_Base <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta)) - length(yv))
}
rsquare_base_intitialized <- 1-exp(-(2/length(yv))*(logLM_Base-logL0))
}
#print(Create.indicator)
#calculate t statistics and P-values
if(i > 0 | file>file.from |frag>1)
{
if(!Create.indicator){
#if(i<5)print(beta[q1])
#if(i<5)print(iXX[q1, q1])
if(!is.null(K)) stats[i, j] <- beta[q1]/sqrt(iXX[q1, q1] *vgs)
if(is.null(K)) stats[i, j] <- beta[q1]/sqrt(iXX[q1, q1] *ves)
effect.est[i, ] <- beta[q1]
ps[i, ] <- 2 * pt(abs(stats[i, ]), dfs[i, ],lower.tail = FALSE)
if(is.na(ps[i,]))ps[i,]=1
#print(c(i,ps[i,],stats[i,],beta[q1],iXX[q1, q1]))
}
if(Create.indicator){
F.num.first.two <- crossprod(beta[(q0+1):q1], solve(iXX[(q0+1):q1,(q0+1):q1]))
if(!is.null(K)) stats[i, j] <- (F.num.first.two %*% beta[(q0+1):q1])/(length((q0+1):q1)*vgs)
if(is.null(K)) stats[i, j] <- (F.num.first.two %*% beta[(q0+1):q1])/(length((q0+1):q1)*ves)
effect.est <- rbind(effect.est, cbind(rep(i,length((q0+1):q1)), indicator$unique.SNPs, beta[(q0+1):q1])) #Replace with rbind
ps[i, ] <- pf(stats[i, j], df1=length((q0+1):q1), df2=(nr-ncol(X)), lower.tail = FALSE) #Alex, are these denominator degrees of freedom correct?
dfs[i,] <- nr-nrow(X)
}
#Calculate the maximum full likelihood function value and the r square
X.beta <- X%*%beta
if(!is.null(K)){
U.times.yv.minus.X.beta <- crossprod(U,(yv-X.beta))
logLM <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta))
- sum(log(eig.full.plus.delta))- length(yv))
}
if(is.null(K)){
U.times.yv.minus.X.beta <- yv-X.beta
logLM <- 0.5*(-length(yv)*log(((2*pi)/length(yv))*crossprod(U.times.yv.minus.X.beta,U.times.yv.minus.X.beta)) - length(yv))
}
rsquare_base[i, ] <- rsquare_base_intitialized
rsquare[i, ] <- 1-exp(-(2/length(yv))*(logLM-logL0))
#Calculate df, t value and standard error _xiaolei changed
df[i,] <- dfs[i,]
tvalue[i,] <- stats[i, j]
stderr[i,] <- beta[ncol(CVI)+1]/stats[i, j]
#stderr[i,] <- sqrt(vgs)
# modified by Jiabo at 20191115
}
#print("!!!!!!!!!!!!!!!")
#print(Create.indicator)
#-------------------------------------------------------------------------------------------------------------------->
} # End of if(normalCase)
x.prev=xv #update SNP
} # End of loop on SNPs
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Screening SNPs")
Memory=GAPIT.Memory(Memory=Memory,Infor="Screening SNPs")
# print(head(tvalue))
# print(head(stderr))
# print(head(effect.est))
#output p value for the genotype file
if(!fullGD)
{
#print("!!!!!!!!!!")
#print(dim(GI))
write.table(GI, paste("GAPIT.TMP.GI.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = TRUE)
write.table(ps, paste("GAPIT.TMP.ps.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(maf, paste("GAPIT.TMP.maf.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(nobs, paste("GAPIT.TMP.nobs.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(rsquare_base, paste("GAPIT.TMP.rsquare.base.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(rsquare, paste("GAPIT.TMP.rsquare.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(df, paste("GAPIT.TMP.df.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(tvalue, paste("GAPIT.TMP.tvalue.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(stderr, paste("GAPIT.TMP.stderr.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
write.table(effect.est, paste("GAPIT.TMP.effect.est.",name.of.trait,file,".",frag,".txt",sep=""), quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
#rm(dfs,stats,ps,nobs,maf,GI) #This cause problem on return
#gc()
}
frag=frag+1 #Progress to next fragment
} #end of if(!is.null(X))
} #end of repeat on fragment
} # Ebd of loop on file
} # End of loop on traits
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GWAS done for this Trait")
Memory=GAPIT.Memory(Memory=Memory,Infor="GWAS done for this Trait")
#print("GAPIT.EMMAxP3D accomplished successfully!")
return(list(ps = ps, REMLs = -2*REMLs, stats = stats, effect.est = effect.est, rsquare_base = rsquare_base, rsquare = rsquare, dfs = dfs, df = df, tvalue = tvalue, stderr = stderr,maf=maf,nobs = nobs,Timmer=Timmer,Memory=Memory,
vgs = vgs, ves = ves, BLUP = BLUP, BLUP_Plus_Mean = BLUP_Plus_Mean,
PEV = PEV, BLUE=BLUE, logLM = logLM,effect.snp=effect.est,effect.cv=beta.cv))
}#end of GAPIT.EMMAxP3D function
#=============================================================================================
`GAPIT.FDR.TypeI` <-
function(WS=c(1e0,1e3,1e4,1e5), GM=NULL,seqQTN=NULL,GWAS=NULL,maxOut=100,MaxBP=1e10){
#Object: To evaluate power and FDR for the top (maxOut) positive interval defined by WS
#Input: WS- window size
#Input: GM - m by 3 matrix for SNP name, chromosome and BP
#Input: seqQTN - s by 1 vecter for index of QTN on GM (+1 for GDP column wise)
#Input: GWAS - SNP,CHR,BP,P,MAF
#maxOut: maximum number of rows to report
#Requirement: None
#Output: Table and Plots
#Authors: Xiaolei Liu & Zhiwu Zhang
# Date start: April 2, 2013
# Last update: Mar 16, 2016
##############################################################################################
#print("GAPIT.Power Started")
if(is.null(seqQTN) | is.null(GM)) return(list(Power=NULL,FDR= NULL,TypeI= NULL,False= NULL,AUC.FDR= NULL,AUC.T1= NULL))
#store number fdr and t1 records
NQTN=length(seqQTN)
table=array(NA,dim=c(NQTN,2*length(WS)))
fdrtable=array(NA,dim=c(NQTN,2*length(WS)))
t1table=array(NA,dim=c(NQTN,2*length(WS)))
cutoff=array(NA,dim=c(length(WS),NQTN))
cut=array(NA,dim=c(1,NQTN))
#-----------------FDR and Power analysis-------------------------
#Information needed: GWAS,myGM and QTN(r)
GWAS=GWAS[order(GWAS[,2],GWAS[,3]),]
GWAS[is.na(GWAS[,4]),4]=1
QTN.list=sort(GWAS[seqQTN,4])
powerlist=seq(1/length(QTN.list),1,length.out=length(QTN.list))
#calculate number of false positives in each WS
total.index=1:nrow(GM)
theWS=1
for (theWS in 1:length(WS)){
wsws=WS[theWS]
qtn.pool=ceiling((as.numeric(GWAS[seqQTN,2])*MaxBP+as.numeric(GWAS[seqQTN,3]))/(2*wsws))
bonf.pool=ceiling((GWAS[total.index,2]*MaxBP+GWAS[total.index,3])/(2*wsws))
false.number=length(levels(factor(bonf.pool[!(bonf.pool%in%qtn.pool)])))
for(j in 1:length(qtn.pool)){
pbin=min(GWAS[bonf.pool==qtn.pool[j],4])
cut[,j]=pbin
}
if(theWS==1){
totalfalse=false.number
}else{
totalfalse=c(totalfalse,false.number)
}
cutoff[theWS,]=sort(cut)
}
#Calculate FDR and T1
for(j in 1:ncol(cutoff)){
theWS=1
for (theWS in 1:length(WS)){
p.index=which(GWAS[,4]<=cutoff[theWS,j])
wsws=WS[theWS]
qtn.pool=ceiling((GWAS[seqQTN,2]*MaxBP+GWAS[seqQTN,3])/(2*wsws))
bonf.pool=ceiling((GWAS[p.index,2]*MaxBP+GWAS[p.index,3])/(2*wsws))
qtn.number=length(levels(factor(bonf.pool[bonf.pool%in%qtn.pool])))
false.number=length(levels(factor(bonf.pool[!(bonf.pool%in%qtn.pool)])))
if(theWS==1){
final=false.number
final.fdr=false.number/(qtn.number+false.number)
final.t1=false.number/totalfalse[theWS]
}else{
record=false.number
record.fdr=false.number/(qtn.number+false.number)
record.t1=false.number/totalfalse[theWS]
final=c(final,record)
final.fdr=c(final.fdr,record.fdr)
final.t1=c(final.t1,record.t1)
}
}
#record FDR and T1
if(j==1){
number.record=final
fdr.record=final.fdr
t1.record=final.t1
}else{
number.record=rbind(number.record,final)
fdr.record=rbind(fdr.record,final.fdr)
t1.record=rbind(t1.record,final.t1)
}
}
table=number.record
fdrtable=fdr.record
t1table=t1.record
#AUC
auc.final.fdr=NULL
auc.final.t1=NULL
for (theWS in 1:length(WS)){
auc.fdr=GAPIT.AUC(beta=powerlist,alpha=fdrtable[,theWS])
auc.t1=GAPIT.AUC(beta=powerlist,alpha=t1table[,theWS])
auc.final.fdr=c(auc.final.fdr,auc.fdr)
auc.final.t1=c(auc.final.t1,auc.t1)
}
return(list(P=cutoff,Power=powerlist,FDR=fdrtable,TypeI=t1table,False=table,AUC.FDR=auc.final.fdr,AUC.T1=auc.final.t1))
}#end of `GAPIT.FDR.TypeI`
#=============================================================================================`GAPIT.FilterByTaxa` <-
function(taxa,Data){
#Object: To filter a data (Y, CV or GD) by taxa
#Input: taxa - vector of taxa
#Input: data - data frame with first column as taxa
#Requirement: all taxa must be in data
#Output: filtered data
#Authors: Zhiwu Zhang
# Last update: May 22, 2013
##############################################################################################
#print("GAPIT.FilterByTaxa Started")
Data=Data[match(taxa, Data[,1], nomatch = 0),]
return (Data)
}#The function GAPIT.FilterByTaxa ends here
#=============================================================================================
`GAPIT.Fragment` <-
function(file.path=NULL,file.from=NULL, file.to=NULL,file.total=NULL,file.G=NULL,
file.Ext.G=NULL,seed=123,SNP.fraction=1,SNP.effect="Add",SNP.impute="Middle",
genoFormat=NULL, file.GD=NULL, file.Ext.GD=NULL, file.GM=NULL, file.Ext.GM=NULL, file.fragment=NULL,
file=1,frag=1,LD.chromosome=NULL,LD.location=NULL,LD.range=NULL, Create.indicator = FALSE, Major.allele.zero = FALSE){
#Object: To load SNPs on a (frag)ment in file (this is to replace sampler)
#Output: genotype data sampled
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: August 18, 2011
##############################################################################################
#print("Fragmental reading...")
genoFormat="hapmap"
if(!is.null(file.GD)&is.null(file.G)) genoFormat="EMMA"
if(genoFormat=="hapmap"){
#Initical G
#print("Reading file...")
G=NULL
if(frag==1){
skip.1=0
G <- try(read.delim(paste(file.path,file.G,file, ".",file.Ext.G,sep=""),
head = FALSE,skip = skip.1, nrows = file.fragment+1),silent=TRUE)
}else{
skip.1 <- (frag-1)*file.fragment +1
G <- try(read.delim(paste(file.path,file.G,file, ".",file.Ext.G,sep=""),
head = FALSE,skip = skip.1, nrows = file.fragment),silent=TRUE )
}
#print("processing the data...")
if(inherits(G, "try-error")) {
G=NULL
#print("File end reached for G!!!")
}
if(is.null(G)){
#print("The above error indicating reading after end of file (It is OK).")
return(list(GD=NULL,GI=NULL,GT=NULL,linesRead=NULL,GLD=NULL,heading=NULL) )
}
#print("Calling hapmap...")
heading=(frag==1)
#Recording number of lineas read
if(heading){
n= nrow(G)-1
}else{
n= nrow(G)
}
linesRead=n
#Sampling
if(SNP.fraction<1){
#print("Number of SNP in this pragment:")
#print(n)
#set.seed(seed+(file*1000)+frag)
#mySample=sample(1:n,max(2,floor(n*as.numeric(as.vector(SNP.fraction)))))
mySample=sample(1:n,max(2,floor(n*SNP.fraction)))
#print("@@@@@@@@@@")
#print(mySample)
#print(length(mySample))
if(heading){
G=G[c(1,(1+mySample)),]
}else{
G=G[mySample,]
}
} #end of if(SNP.fraction<1)
print("Call hapmap from fragment")
hm=GAPIT.HapMap(G,SNP.effect=SNP.effect,SNP.impute=SNP.impute,heading=heading, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
#print("Extracting snps for LD plot...")
#Extract SNPs for LD plot
if(!is.null(LD.chromosome) & !is.null(hm$GD)){
index=(G[,3]==LD.chromosome[1]) & abs((as.numeric(G[,4])-as.numeric(LD.location[1]))<(as.numeric(LD.range[1])/2))
GLD=G[index,]
}else{
GLD=NULL
}
#rm(G)
#gc()
print("hapmap called successfuly from fragment")
return(list(GD=hm$GD,GI=hm$GI,GT=hm$GT,linesRead=linesRead,GLD=GLD,heading=heading,G=G))
print("ERROR: It should not get here!!!")
} #end of "hapmap"
if(genoFormat=="EMMA"){
#print("The file is a numerical format!")
#Initial GD
GD=NULL
skip.1 <- (frag-1)*file.fragment
#Skip the remaining columns
GD.temp <- try(read.table(paste(file.path,file.GD, file, ".", file.Ext.GD,sep=""), head = TRUE, nrows = 1),silent=TRUE)
num.SNP <- ncol(GD.temp)-1
rm(GD.temp)
read.in <- min(file.fragment,(num.SNP-skip.1))
skip.2 <- max((num.SNP - (skip.1 + read.in)),0)
print(paste(file.path,file.GD,file, ".",file.Ext.GD,sep=""))
GD <- try(read.table(paste(file.path,file.GD,file, ".",file.Ext.GD,sep=""), head = TRUE,
colClasses = c("factor", rep("NULL", skip.1), rep("numeric", read.in),
rep("NULL", skip.2))) ,silent=TRUE)
GI <- try(read.table(paste(file.path,file.GM,file, ".",file.Ext.GM,sep=""), head = TRUE,
skip=skip.1, nrows=file.fragment) ,silent=TRUE)
if(inherits(GD, "try-error")) {
GD=NULL
print("File end reached for GD!!!")
}
if(inherits(GI, "try-error")) {
GI=NULL
print("File end reached for GI!!!")
}
if(is.null(GD)) return(list(GD=NULL, GI=NULL,GT=NULL,linesRead=NULL,GLD=NULL))
GT=GD[,1] #Extract infividual names
GD=GD[,-1] #Remove individual names
#print("Numerical file read sucesfuly from fragment")
linesRead=ncol(GD)
if(SNP.fraction==1) return(list(GD=GD, GI=GI,GT=GT,linesRead=linesRead,GLD=NULL))
if(SNP.fraction<1){
n= ncol(GD)
#set.seed(seed+file)
sample=sample(1:n,floor(n*SNP.fraction))
return(list(GD=GD[,sample], GI=GI[sample,],GT=GT,linesRead=linesRead,GLD=NULL))
}
} # end of the "EMMA"
#print("fragment ended succesfully!")
}#End of fragment
#=============================================================================================
`GAPIT.GS` <-
function(KW,KO,KWO,GAU,UW){
#Object: to derive BLUP for the individuals without phenotype
#UW:BLUP and PEV of ID with phenotyp
#Output: BLUP
#Authors: Zhiwu Zhang
# Last update: Oct 22, 2015 by Jiabo Wang
##############################################################################################
#print(dim(UW))
UO=try(t(KWO)%*%solve(KW)%*%UW,silent=TRUE)
#print(dim(KWO)) #kinship without inference
#print(dim(KW)) #kinship within inference
#print(dim(UW)) #BLUP AND PEV of reference
if(inherits(UO, "try-error")) UO=t(KWO)%*%ginv(KW)%*%UW
n=ncol(UW) #get number of columns, add additional for individual name
BLUP=data.frame(as.matrix(GAU[,1:4]))
BLUP.W=BLUP[which(GAU[,3]<2),]
W_BLUP=BLUP.W[order(as.numeric(as.matrix(BLUP.W[,4]))),]
UW=UW[which(rownames(UW)==colnames(KW)),] # get phenotype groups order
ID.W=as.numeric(as.matrix(W_BLUP[,4]))
n.W=max(ID.W)
DS.W=diag(n.W)[ID.W,]
ind.W=DS.W%*%UW
all.W=cbind(W_BLUP,ind.W)
all=all.W
BLUP.O=BLUP[which(GAU[,3]==2),]
O_BLUP=BLUP.O[order(as.numeric(as.matrix(BLUP.O[,4]))),]
#print(dim(O_BLUP))
if(nrow(O_BLUP)>0){
ID.O=as.numeric(as.matrix(O_BLUP[,4]))
n.O=max(ID.O)
DS.O=diag(n.O)[ID.O,]
ind.O=DS.O%*%UO
all.O=cbind(O_BLUP,ind.O)
all=rbind(all.W,all.O)
}
colnames(all)=c("Taxa", "Group", "RefInf","ID","BLUP","PEV")
print("GAPIT.GS accomplished successfully!")
return(list(BLUP=all))
}#The function GAPIT.GS ends here
#=============================================================================================
`GAPIT.GS.Visualization` <-
function(gsBLUP = gsBLUP, BINS=BINS, name.of.trait = name.of.trait){
#Object: To build heat map to show distribution of BLUP and PEV
#Output: pdf
#Authors: Zhiwu Zhang
# Last update: May 15, 2011
##############################################################################################
nBin=BINS
BLUP= gsBLUP[,5]
PEV = gsBLUP[,6]
if(BLUP[1]=="NaN"){
warning ("It was not converged. BLUP was not created!")
}
if(BLUP[1]!="NaN" )
{
BLUP.max=try(max(BLUP))
BLUP.min=try(min(BLUP))
if(inherits(BLUP.max, "try-error")) return()
range.BLUP=BLUP.max-BLUP.min
range.PEV=max(PEV)-min(PEV)
interval.BLUP=range.BLUP/nBin
interval.PEV=range.PEV/nBin
bin.BLUP=floor(BLUP/max(BLUP)*nBin)*max(BLUP)/nBin
bin.PEV=floor(PEV/max(PEV)*nBin)*max(PEV)/nBin
distinct.BLUP=unique(bin.BLUP)
distinct.PEV=unique(bin.PEV)
if((length(distinct.BLUP)<2) | (length(distinct.PEV)<2) ) return() #nothing to plot
Position.BLUP=match(bin.BLUP,distinct.BLUP,nomatch = 0)
Position.PEV=match(bin.PEV,distinct.PEV,nomatch = 0)
value=matrix(1,length(Position.BLUP))
KG<- (tapply(as.numeric(value), list(Position.BLUP, Position.PEV), sum))
rownames(KG)=round(distinct.BLUP, digits = 4)
colnames(KG)=round(distinct.PEV, digits = 4)
#Sort the rows and columns in order from smallest to largest
rownames(KG) <- rownames(KG)[order(as.numeric(rownames(KG)))]
colnames(KG) <- colnames(KG)[order(as.numeric(colnames(KG)))]
rownames(KG) <- round(as.numeric(rownames(KG)))
colnames(KG) <- round(as.numeric(colnames(KG)))
#write.table(KG, "Input_Matrix_for_GS_Heat_Map.txt", quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
pdf(paste("GAPIT.", name.of.trait,".GPS.BLUPvsPEV", ".pdf", sep = ""),width = 9)
#par(mfrow = c(1,1), mar = c(1,1,5,5), lab = c(5,5,7))
par(mar = c(5,5,6,5))
nba_heatmap <- heatmap.2(KG, Rowv=NA, Colv=NA, col = rev(heat.colors(256)), # scale="column",
xlab = "PEV", ylab = "BLUP", main = " ", scale="none", symkey=FALSE, trace="none")
#nba_heatmap <- heatmap.2(KG, cexRow =.2, cexCol = 0.2, scale="none", symkey=FALSE, trace="none" )
#cexRow =0.9, cexCol = 0.9)
dev.off()
}
#print("GAPIT.GS.Visualization accomplished successfully!")
} #GAPIT.GS.Visualization ends here
#=============================================================================================
`GAPIT.Genotype` <-
function(G=NULL,GD=NULL,GM=NULL,KI=NULL,
kinship.algorithm="Zhang",SNP.effect="Add",SNP.impute="Middle",PCA.total=0,PCA.col=NULL,PCA.3d=PCA.3d,seed=123, SNP.fraction =1,
file.path=NULL,file.from=NULL, file.to=NULL, file.total=NULL, file.fragment = 1000,SNP.test=TRUE,
file.G =NULL,file.Ext.G =NULL,
file.GD=NULL,file.Ext.GD=NULL,
file.GM=NULL,file.Ext.GM=NULL,
SNP.MAF=0.05,FDR.Rate = 0.05,SNP.FDR=1,
Timmer=NULL,Memory=NULL,
LD.chromosome=NULL,LD.location=NULL,LD.range=NULL, SNP.CV=NULL,
GP = NULL,GK = NULL,GTindex=NULL,
bin.size = 1000,inclosure.size = 100,
sangwich.top=NULL,sangwich.bottom=NULL,
file.output=TRUE,kinship.cluster="average",NJtree.group=NULL,NJtree.type=c("fan","unrooted"),
Create.indicator = FALSE, Major.allele.zero = FALSE,Geno.View.output=TRUE){
#Object: To unify genotype and calculate kinship and PC if required:
# 1.For G data, convert it to GD and GI
# 2.For GD and GM data, nothing change
# 3.Samling GD and create KI and PC
# 4.Go through multiple files
# 5.In any case, GD must be returned (for QC)
#Output: GD, GI, GT, KI and PC
#Authors: Zhiwu Zhang
#Last update: August 11, 2011
##############################################################################################
#print("Genotyping: numericalization, sampling kinship, PCs and much more...")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype start")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype start")
#Create logical variables
byData=!is.null(G) | !is.null(GD)
byFile=!is.null(file.G) | !is.null(file.GD)
hasGenotype=(byData | byFile )
needKinPC=(is.null(KI) | PCA.total>0 | kinship.algorithm=="Separation")
if(!is.null(KI) & !byData & !byFile & !SNP.test &kinship.algorithm!="SUPER") {
print("It return unexpected")
return (list(GD=NULL,GI=NULL,GT=NULL,hasGenotype=FALSE, genoFormat=NULL, KI=KI,PC=NULL,byFile=FALSE,fullGD=TRUE,Timmer=Timmer,Memory=Memory))
}
#Set indicator for full GD
fullGD=FALSE
if(byData) fullGD=TRUE
if(byFile & SNP.fraction==1 & needKinPC) fullGD=TRUE
#SET GT to NULL in case of no genotype
if(!byData & !byFile & is.null(GK) &kinship.algorithm!="SUPER") {
if(is.null(KI) & is.null(GP) & is.null(GK)) stop("GAPIT says: Kinship has to be provided or estimated from genotype!!!")
return (list(GD=NULL,GI=NULL,GT=NULL,hasGenotype=FALSE, genoFormat=NULL, KI=KI,PC=NULL,byFile=FALSE,fullGD=TRUE,Timmer=Timmer,Memory=Memory))
}
genoFormat="hapmap"
if(is.null(G)&is.null(file.G)) genoFormat="EMMA"
#Multiple genotype files
#In one of the 3 situations, calculate KI with the algorithm specified, otherwise skip cit by setting algorithm to "SUPER"
kinship.algorithm.save=kinship.algorithm
kinship.algorithm="SUPER"
#Normal
if(is.null(sangwich.top) & is.null(sangwich.bottom) ) kinship.algorithm=kinship.algorithm.save
#TOP or Bottom is MLM
pass.top=FALSE
if(!is.null(sangwich.top)) pass.top=!(sangwich.top=="FaST" | sangwich.top=="SUPER" | sangwich.top=="DC")
pass.bottom=FALSE
if(!is.null(sangwich.bottom)) pass.bottom=!(sangwich.bottom=="FaST" | sangwich.bottom=="SUPER" | sangwich.bottom=="DC")
if(pass.top | pass.bottom )kinship.algorithm=kinship.algorithm.save
#Compatibility of input
#agreement among file from, to and total
if(!is.null(file.from) &!is.null(file.to) &!is.null(file.total)){
if(file.total!=(file.to-file.from+1)) stop("GAPIT says: Conflict among file (from, to and total)")
}
if(!is.null(file.from) &!is.null(file.to)) {
if(file.to<file.from) stop("GAPIT says: file.from should smaller than file.to")
}
#file.from and file.to must be in pair
if(is.null(file.from) &!is.null(file.to) ) stop("GAPIT says: file.from and file.to must be in pair)")
if(!is.null(file.from) &is.null(file.to) ) stop("GAPIT says: file.from and file.to must be in pair)")
#assign file.total
if(!is.null(file.from) &!is.null(file.to) ) file.total=file.to-file.from+1
if(byFile& is.null(file.total)) stop("GAPIT says: file.from and file.to must be provided!)")
if(!is.null(GP) & !is.null(GK) ) stop("GAPIT Says: You can not provide GP and GK at same time")
if(!is.null(GP) & !is.null(KI) ) stop("GAPIT Says: You can not provide GP and KI at same time")
if(!is.null(GK) & !is.null(KI)) stop("GAPIT says: You can not specify GK and KI at same time!!!")
#GP does not allow TOP
if(!is.null(GP) & !is.null(sangwich.top) ) stop("GAPIT Says: You provided GP. You can not spycify sangwich.top")
#Top require a bottom
if(!is.null(sangwich.top) & is.null(sangwich.bottom) ) stop("GAPIT Says: Top require its Bottom")
#naked bottom require GP or GK
if(is.null(sangwich.top) & !is.null(sangwich.bottom) & (is.null(GP) & is.null(GK)) ) stop("GAPIT Says: Uncovered Bottom (without TOP) requires GP or GK")
#Pseudo top (GK or GP) requires a bottom
if(is.null(sangwich.top) & is.null(sangwich.bottom) & (!is.null(GP)|!is.null(GK ))) stop("GAPIT Says: You have provide GP or GK, you need to provide Bottom")
#if(!is.null(KI) &!is.null(kinship.algorithm)) stop("GAPIT says: You can not specify kinship.algorithm and provide kinship at same time!!!")
if(!needKinPC &SNP.fraction<1) stop("GAPIT says: You did not require calculate kinship or PCs. SNP.fraction should not be specified!!!")
if(!SNP.test & is.null(KI) & !byData & !byFile) stop("GAPIT says: For SNP.test optioin, please input either use KI or use genotype")
#if(is.null(file.path) & !byData & byFile) stop("GAPIT Ssays: A path for genotype data should be provided!")
if(is.null(file.total) & !byData & byFile) stop("GAPIT Ssays: Number of file should be provided: >=1")
if(!is.null(G) & !is.null(GD)) stop("GAPIT Ssays: Both hapmap and EMMA format exist, choose one only.")
if(!is.null(file.GD) & is.null(file.GM) & (!is.null(GP)|!is.null(GK)) ) stop("GAPIT Ssays: Genotype data and map files should be in pair")
if(is.null(file.GD) & !is.null(file.GM) & (!is.null(GP)|!is.null(GK)) ) stop("GAPIT Ssays: Genotype data and map files should be in pair")
if(!is.null(GD) & is.null(GM) & (is.null(GP)&is.null(GK)) &kinship.algorithm!="SUPER") stop("GAPIT Says: Genotype data and map files should be in pair")
if(is.null(GD) & !is.null(GM) & (is.null(GP)&is.null(GK)) &kinship.algorithm!="SUPER") stop("GAPIT Says: Genotype data and map files should be in pair")
#if(!byData & !byFile) stop("APIT Ssays: Either genotype data or files should be given!")
#if(byData&(!is.null(file.path))) stop ("APIT Ssays: You have provided geotype data. file.path should not be provided!")
#print("Pass compatibility of input")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype loaded")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype loaded")
#Inital GLD
GLD=NULL
SNP.QTN=NULL #Intitial
GT=NULL
#Handler of read data in numeric format (EMMA)
#Rename GM as GI
if(!is.null(GM))GI=GM
rm(GM)
gc()
#Extract GD and GT from read data GD
if(!is.null(GD) )
{
GT=as.matrix(GD[,1]) #get taxa
GD=as.matrix(GD[,-1]) #remove taxa column
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GT created from GD)")
Memory=GAPIT.Memory(Memory=Memory,Infor="GT created from GD")
}
#Hapmap format
if(!is.null(G))
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before HapMap")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before HapMap")
#Convert HapMap to numerical
print(paste("Converting genotype...",sep=""))
hm=GAPIT.HapMap(G,SNP.effect=SNP.effect,SNP.impute=SNP.impute, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="after HapMap")
Memory=GAPIT.Memory(Memory=Memory,Infor="after HapMap")
#Extracting SNP for LD plot
if(!is.null(LD.chromosome)){
#print("Extracting SNP for LD plot...")
chromosome=(G[,3]==LD.chromosome[1])
bp=as.numeric(as.vector(G[,4]))
deviation=abs(bp-as.numeric(as.vector(LD.location[1])) )
location=deviation< as.numeric(as.vector(LD.range[1]) )
index=chromosome&location
GLD=G[index,]
}else{
#print("No data in GLD")
GLD=NULL
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="HapMap")
Memory=GAPIT.Memory(Memory=Memory,Infor="HapMap")
print(paste("Converting genotype done.",sep=""))
#rm(G)
#gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="G removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="G removed")
GT=hm$GT
GD=hm$GD
GI=hm$GI
#print(unique(GI[,2]))
rm(hm)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="hm removed")
Memory=GAPIT.Memory(Memory=Memory,Infor="hm removed")
}
#From files
if(!byData & byFile){
#print("Loading genotype from files...")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="byFile")
Memory=GAPIT.Memory(Memory=Memory,Infor="byFile")
numFileUsed=file.to
if(!needKinPC)numFileUsed=file.from
#Initial GI as storage
GD=NULL
GT=NULL
GI=NULL
GLD=NULL
#multiple fragments or files
for (file in file.from:numFileUsed){
frag=1
numSNP=file.fragment
myFRG=NULL
#print(paste("numSNP before while is ",numSNP))
while(numSNP==file.fragment) { #this is problematic if the read end at the last line
print(paste("Reading file: ",file,"Fragment: ",frag))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before Fragment")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before Fragment")
myFRG=GAPIT.Fragment( file.path=file.path,file.from=file.from, file.to=file.to,file.total=file.total,file.G=file.G,file.Ext.G=file.Ext.G,
seed=seed,SNP.fraction=SNP.fraction,SNP.effect=SNP.effect,SNP.impute=SNP.impute,genoFormat=genoFormat,
file.GD=file.GD,file.Ext.GD=file.Ext.GD,file.GM=file.GM,file.Ext.GM=file.Ext.GM,
file.fragment=file.fragment,file=file,frag=frag,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
#print(paste("numSNP after while is ",numSNP))
#print(paste("OK with file: ",file,"Fragment: ",frag))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="After Fragment")
Memory=GAPIT.Memory(Memory=Memory,Infor="After Fragment")
if(is.null(GT) & !is.null(myFRG$GT))GT= as.matrix(myFRG$GT)
if(is.null(GD)){
GD= myFRG$GD
}else{
if(!is.null(myFRG$GD)) {
GD=cbind(GD,myFRG$GD)
}
}
if(is.null(GI)){
GI= myFRG$GI
}else{
if(!is.null(myFRG$GI)) {
colnames(myFRG$GI)=c("SNP","Chromosome","Position")
GI=as.data.frame(rbind(as.matrix(GI),as.matrix(myFRG$GI)))
}
}
if(is.null(G)){
G= myFRG$G
}else{
if(!is.null(myFRG$G)) {
G=as.data.frame(rbind(as.matrix(G),as.matrix(myFRG$G[-1,])))
}
}
if(is.null(GLD)){
GLD= myFRG$GLD
}else{
if(!is.null(myFRG$GLD)) {
if(myFRG$heading){
GLD=as.data.frame(rbind(as.matrix(GLD),as.matrix(myFRG$GLD[-1,])))
}else{
GLD=as.data.frame(rbind(as.matrix(GLD),as.matrix(myFRG$GLD)))
}
}
}
#print("This fragment is joined")
if(file==file.from & frag==1)GT=as.matrix(myFRG$GT)
frag=frag+1
if(!is.null(myFRG$GI)) {
numSNP=myFRG$linesRead[1]
}else{
numSNP=0
}
if(!needKinPC)numSNP=0 #force to end the while loop
if(is.null(myFRG))numSNP=0 #force to end the while loop
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="END this Fragment")
Memory=GAPIT.Memory(Memory=Memory,Infor="END this Fragment")
} #end of repeat on fragment
# print("This file is OK")
} #end of file loop
print("All files loaded")
} #end of if(!byData&byFile)
#GM=as.matrix(GI)
#GI=GM
GM=GI
#print(unique(GM[,2]))
#print("@@@@@@@@@@")
#Set the number of chromosome
# if(1%in%as.character(unique(GM[,2])))
# { chor_taxa=mixedsort(as.character((unique(GM[,2]))))
# }else{
# chor_taxa=as.character(unique(GM[,2]))
# #print(chor_taxa)
# for(i in 1:(length(chor_taxa)))
# {
# index=GM[,2]==chor_taxa[i]
# GI[index,2]=i
# }
# }
# modified by Jiabo in 20190927. sorted number of chrom by numeric and charicter
chor_taxa=as.character(unique(GM[,2]))
chor_taxa[order(gsub("([A-Z]+)([0-9]+)", "\\1", chor_taxa),
as.numeric(gsub("([A-Z]+)([0-9]+)", "\\2", chor_taxa)))]
chr_letter=grep("[A-Z]|[a-z]",chor_taxa)
if(!setequal(integer(0),chr_letter))
{
GI=as.matrix(GI)
for(i in 1:(length(chor_taxa)))
{
index=GM[,2]==chor_taxa[i]
GI[index,2]=i
}
}
#print(head(GI))
#print(head(GI))
#print("@@@@@@@@@@@")
#print(GD[1:5,1:5])
#print(dim(GI))
#Follow the MAF to filter markers
if(!is.null(GD))
{
#maf=apply(as.matrix(GD),2,function(one) abs(1-sum(one)/(2*nrow(GD))))
#maf[maf>0.5]=1-maf[maf>0.5]
ss=apply(GD,2,sum)
maf=apply(cbind(.5*ss/(nrow(GD)),1-.5*ss/(nrow(GD))),1,min)
#print(max(maf))
#print(min(maf))
maf_index=maf>=SNP.MAF
print(paste("GAPIT will filter marker with MAF setting !!"))
print(paste("The markers will be filtered by SNP.MAF: ",SNP.MAF,sep=""))
print(table(maf_index))
#print(head(maf[!maf_index]))
GD=GD[,maf_index]
GM=as.data.frame(GI[maf_index,])
GI=GM
}
#print("file loaded")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Sampling genotype")
Memory=GAPIT.Memory(Memory=Memory,Infor="Sampling genotype")
#print(KI)
#Plot thirt part kinship
if(!is.null(KI) &file.output) {
if(KI!=1) {
if(nrow(KI)<1000){
print("Plotting Kinship")
#print(dim(KI))
theKin=as.matrix(KI[,-1])
line.names <- KI[,1]
colnames(theKin)=KI[,1]
rownames(theKin)=KI[,1]
distance.matrix=dist(theKin,upper=TRUE)
hc=hclust(distance.matrix,method=kinship.cluster)
hcd = as.dendrogram(hc)
##plot NJtree
if (!is.null(NJtree.group))
{
clusMember <- cutree(hc, k = NJtree.group)
compress_z=table(clusMember,paste(line.names))
type_col=rainbow(NJtree.group)
#type_col=rainbow(NJtree.group)
Optimum=c(nrow(theKin),kinship.cluster,NJtree.group)
#rm(distance.matrix,hc)
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="set kinship")
Memory=GAPIT.Memory(Memory=Memory,Infor="set kinship")
print("Creating heat map for kinship...")
pdf(paste("GAPIT.Kin.thirdPart.pdf",sep=""), width = 12, height = 12)
par(mar = c(25,25,25,25))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="prepare heatmap")
Memory=GAPIT.Memory(Memory=Memory,Infor="prepare heatmap")
heatmap.2(theKin, cexRow =.2, cexCol = 0.2, col=rev(heat.colors(256)), scale="none", symkey=FALSE, trace="none")
dev.off()
print("Kinship heat map PDF created!")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="plot heatmap")
Memory=GAPIT.Memory(Memory=Memory,Infor="plot heatmap")
## Jiabo Wang add NJ Tree of kinship at 4.5.2017
if (!is.null(NJtree.group))
{
for(tr in 1:length(NJtree.type))
{
print("Creating NJ Tree for kinship...")
pdf(paste("GAPIT.Kin.NJtree.",NJtree.type[tr],".pdf",sep=""), width = 12, height = 12)
par(mar = c(5,5,5,5))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="prepare NJ TREE")
Memory=GAPIT.Memory(Memory=Memory,Infor="prepare NJ TREE")
plot(as.phylo(hc), type = NJtree.type[tr], tip.color =type_col[clusMember], use.edge.length = TRUE, col = "gray80",cex=0.6)
#legend("topright",legend=c(paste("Tatal numerber of individuals is ",),lty=0,cex=1.3,bty="n",bg=par("bg"))
legend("topright",legend=paste(c("Tatal individuals is: ","Cluster method: ","Group number: "), Optimum[c(1:3)], sep=""),lty=0,cex=1.3,bty="n",bg=par("bg"))
dev.off()
}
write.table(compress_z,paste("GAPIT.Kin.NJtree.compress_z.txt",sep=""),quote=F)
print("Kinship NJ TREE PDF created!")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="plot NJ TREE")
Memory=GAPIT.Memory(Memory=Memory,Infor="plot NJ TREE")
#rm(hc,clusMember)
}#end
## NJ Tree end
} #end of if(nrow(KI)<1000)
} #end of if(KI!=1)
} #end of if(!is.null(KI))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before SUPER")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before SUPER")
#SUPER
if(!is.null(GP) & kinship.algorithm=="SUPER" & !is.null(bin.size) & !is.null(inclosure.size)){
mySpecify=GAPIT.Specify(GI=GI,GP=GP,bin.size=bin.size,inclosure.size=inclosure.size)
SNP.QTN=mySpecify$index
if(!is.null(GD)){
#comment out to keep all taxa for GS, Zhiwu (Dec7, 2012)
#GK=GD[GTindex,SNP.QTN]
#SNPVar=apply(as.matrix(GK),2,var)
#GK=GK[,SNPVar>0]
#GK=cbind(as.data.frame(GT[GTindex]),as.data.frame(GK)) #add taxa
GK=GD[,SNP.QTN]
SNPVar=apply(as.matrix(GK),2,var)
GK=GK[,SNPVar>0]
GK=cbind(as.data.frame(GT),as.data.frame(GK)) #add taxa
#print("QTN extracted")
}
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before creating kinship")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before creating kinship")
#Create kinship from genotype if not provide
if(is.null(KI) & (!is.null(GD) |!is.null(GK)) & !kinship.algorithm%in%c("FarmCPU","Blink","MLMM"))
{
print("Calculating kinship...")
if(!is.null(GK)){
thisGD=GK[,-1]
myGT=as.matrix(GK[,1])
print("GK is used to create KI")
}else{
thisGD=GD
myGT=GT
#comment out to keep all taxa for GS, Zhiwu (Dec7, 2012)
#if(!is.null(GTindex)){
# thisGD=thisGD[GTindex,]
# myGT=myGT[GTindex]
#}
}
print(paste("Number of individuals and SNPs are ",nrow(thisGD)," and ",ncol(thisGD)))
theKin=NULL
if(kinship.algorithm=="EMMA"){
half.thisGD = as.matrix(.5*thisGD)
if(length(which(is.na(half.thisGD))) > 0){
print("Substituting missing values with heterozygote for kinship matrrix calculation....")
half.thisGD[which(is.na(half.thisGD))] = 1
}
theKin= emma.kinship(snps=t(as.matrix(.5*thisGD)), method="additive", use="all")
}
if(kinship.algorithm=="Loiselle")theKin= GAPIT.kinship.loiselle(snps=t(as.matrix(.5*thisGD)), method="additive", use="all")
if(kinship.algorithm=="VanRaden")theKin= GAPIT.kinship.VanRaden(snps=as.matrix(thisGD))
if(kinship.algorithm=="Zhang")theKin= GAPIT.kinship.ZHANG(snps=as.matrix(thisGD))
if(kinship.algorithm=="Separation")theKin= GAPIT.kinship.separation(PCs=thePCA$PCs,EV=thePCA$EV,nPCs=PCA.total)
if(!is.null(theKin)){
colnames(theKin)=myGT
rownames(theKin)=myGT
line.names <- myGT
if (!is.null(NJtree.group))
{
distance.matrix=dist(theKin,upper=TRUE)
hc=hclust(distance.matrix,method=kinship.cluster)
hcd = as.dendrogram(hc)
clusMember <- cutree(hc, k = NJtree.group)
compress_z=table(clusMember,paste(line.names))
type_col=rainbow(NJtree.group)
Optimum=c(nrow(theKin),kinship.cluster,NJtree.group)
}
#print(Optimum)
print("kinship calculated")
if(length(GT)<1000 &file.output){
#Create heat map for kinship
print("Creating heat map for kinship...")
pdf(paste("GAPIT.Kin.",kinship.algorithm,".pdf",sep=""), width = 12, height = 12)
par(mar = c(25,25,25,25))
heatmap.2(theKin, cexRow =.2, cexCol = 0.2, col=rev(heat.colors(256)), scale="none", symkey=FALSE, trace="none")
dev.off()
print("Kinship heat map created")
## Jiabo Wang add NJ Tree of kinship at 4.5.2017
if (!is.null(NJtree.group))
{
print("Creating NJ Tree for kinship...")
for(tr in 1:length(NJtree.type))
{
pdf(paste("GAPIT.Kin.NJtree.",NJtree.type[tr],".pdf",sep=""), width = 12, height = 12)
par(mar = c(0,0,0,0))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="prepare NJ TREE")
Memory=GAPIT.Memory(Memory=Memory,Infor="prepare NJ TREE")
plot(as.phylo(hc), type = NJtree.type[tr], tip.color =type_col[clusMember], use.edge.length = TRUE, col = "gray80",cex=0.6)
#legend("topright",legend=c(paste("Tatal numerber of individuals is ",),lty=0,cex=1.3,bty="n",bg=par("bg"))
legend("topright",legend=paste(c("Tatal individuals is: ","Group method: ","Group number: "), Optimum[c(1:3)], sep=""),lty=0,cex=1.3,bty="n",bg=par("bg"))
dev.off()
}
# print(Optimum)
write.table(compress_z,paste("GAPIT.Kin.NJtree.compress_z.txt",sep=""),quote=F)
print("Kinship NJ TREE PDF created!")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="plot NJ TREE")
Memory=GAPIT.Memory(Memory=Memory,Infor="plot NJ TREE")
rm(hc)
}#end NJtree
}
print("Adding IDs to kinship...")
#Write the kinship into a text file
KI=cbind(myGT,as.data.frame(theKin)) #This require big memory. Need a way to solve it.
print("Writing kinship to file...")
if(file.output) write.table(KI, paste("GAPIT.Kin.",kinship.algorithm,".csv",sep=""), quote = FALSE, sep = ",", row.names = FALSE,col.names = FALSE)
print("Kinship save as file")
rm(theKin)
gc()
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Estimating kinship")
Memory=GAPIT.Memory(Memory=Memory,Infor="Estimating kinship")
print("Kinship created!")
} #end of if(is.null(KI)&!is.null(GD))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="after creating kinship")
Memory=GAPIT.Memory(Memory=Memory,Infor="after creating kinship")
#LD plot
#print("LD section")
if(!is.null(GLD) &file.output){
if(nrow(GLD)>500){
GLD=GLD[1,]
print("WARNING: The number of SNPs requested is beyond limitation. No LD plot created.")
}
if(nrow(GLD)>1)
{
print("Plot LD...")
hapmapgeno= data.frame(as.matrix(t(GLD[,-c(1:11)])))
hapmapgeno[hapmapgeno=="NN"]=NA
hapmapgeno[hapmapgeno=="XX"]=NA
hapmapgeno[hapmapgeno=="--"]=NA
hapmapgeno[hapmapgeno=="++"]=NA
hapmapgeno[hapmapgeno=="//"]=NA
LDdist=as.numeric(as.vector(GLD[,4]))
LDsnpName=GLD[,1]
colnames(hapmapgeno)=LDsnpName
#Prune SNM names
#LDsnpName=LDsnpName[GAPIT.Pruning(LDdist,DPP=7)]
LDsnpName=LDsnpName[c(1,length(LDsnpName))] #keep the first and last snp names only
#print(hapmapgeno)
print("Getting genotype object")
LDsnp=makeGenotypes(hapmapgeno,sep="",method=as.genotype) #This need to be converted to genotype object
print("Caling LDheatmap...")
pdf(paste("GAPIT.LD.chromosom",LD.chromosome,"(",round(max(0,LD.location-LD.range)/1000000),"_",round((LD.location+LD.range)/1000000),"Mb)",".pdf",sep=""), width = 12, height = 12)
#pdf(paste("GAPIT.LD.pdf",sep=""), width = 12, height = 12)
par(mar = c(25,25,25,25))
MyHeatmap <- try(LDheatmap(LDsnp, LDdist, LDmeasure="r", add.map=TRUE,
SNP.name=LDsnpName,color=rev(cm.colors(20)), name="myLDgrob", add.key=TRUE,geneMapLabelY=0.1) )
if(!inherits(MyHeatmap, "try-error")) {
#Modify the plot
grid.edit(gPath("myLDgrob", "Key", "title"), gp=gpar(cex=.5, col="blue")) #edit key title size and color
grid.edit(gPath("myLDgrob", "geneMap", "title"), gp=gpar(just=c("center","bottom"), cex=0.8, col="black")) #Edit gene map title
grid.edit(gPath("myLDgrob", "geneMap","SNPnames"), gp = gpar(cex=0.3,col="black")) #Edit SNP name
}else{
print("Warning: error in converting genotype. No LD plot!")
}
dev.off()
print("LD heatmap crated")
#grid.edit(gPath("myLDgrob", "heatMap","title"), gp=gpar(cex=1.0)) #Make title smaler
#grid.edit(gPath("myLDgrob", "geneMap", "title"), gp=gpar(just=c("right","bottom"), cex=0.5, col="blue")) #Edit gene map title
#grid.edit(gPath("myLDgrob", "Key", "labels"), gp=gpar(cex=.5, col="black")) #edit key lable size and color
}else{ # alternative of if(nrow(GLD)>1)
print("Warning: There are less than two SNPs on the region you sepcified. No LD plot!")
} #end of #if(nrow(GLD)>1)
}#end of if(!is.null(GLD))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="after LD plot")
Memory=GAPIT.Memory(Memory=Memory,Infor="after LD plot")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Before PCA")
Memory=GAPIT.Memory(Memory=Memory,Infor="Before PCA")
#Create PC
#print(PCA.total)
PC=NULL
thePCA=NULL
if(is.null(PCA.col)&!is.null(NJtree.group))PCA.col=type_col[clusMember]
#print("!!!!!!!!!!")
#print(PCA.col)
if(PCA.total>0 | kinship.algorithm=="Separation"){
thePCA=GAPIT.PCA(X = GD, taxa = GT, PC.number = PCA.total,file.output=file.output,PCA.total=PCA.total,PCA.col=PCA.col,PCA.3d=PCA.3d)
PC=thePCA$PCs[,1:(1+PCA.total)]
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PCA")
Memory=GAPIT.Memory(Memory=Memory,Infor="PCA")
print("PC created")
}
###output Marker density and decade of linkage disequilibrium over distance
if(!is.null(GI) & !is.null(GD) & file.output & Geno.View.output){
ViewGenotype<-GAPIT.Genotype.View(
myGI=GI,
myGD=GD,
#chr=1,
#w1_start=30,
#w1_end=230,
#mav1=10
)
}
#print("Genotype successfully acomplished")
return (list(G=G,GD=GD,GI=GI,GT=GT,hasGenotype=hasGenotype, genoFormat=genoFormat, KI=KI,PC=PC,byFile=byFile,fullGD=fullGD,Timmer=Timmer,Memory=Memory,SNP.QTN=SNP.QTN,chor_taxa=chor_taxa))
}
#=============================================================================================
`GAPIT.Genotype.View` <-function(myGI=NULL,myGD=NULL,chr=NULL, w1_start=NULL,w1_end=NULL,mav1=NULL){
# Object: Analysis for Genotype data:Distribution of SNP density,Accumulation,Moving Average of density,result:a pdf of the scree plot
# myG:Genotype data
# chr: chromosome value
# w1_start:Moving Average windows Start Position
# w1_end:Moving Average windows End Position
# mav1:Moving Average set value length
# Authors: You Tang and Zhiwu Zhang
# Last update: March 11, 2016
##############################################################################################
#if(nrow(myGI)<1000) return() #Markers are not enough for this analysis
if(is.null(myGI)){stop("Validation Invalid. Please select read valid Genotype flies !")}
if(is.null(myGD)){stop("Validation Invalid. Please select read valid Genotype flies !")}
if(is.null(w1_start)){w1_start=1}
##if(is.null(w1_end)){w1_end=100}
if(is.null(mav1)){mav1=10}
if(is.null(chr)){chr=1}
#heterozygosity of individuals and SNPs (By Zhiwu Zhang)
#print("Heterozygosity of individuals and SNPs (By Zhiwu Zhang)")
X=myGD[,-1]
H=1-abs(X-1)
het.ind=apply(H,1,mean)
het.snp=apply(H,2,mean)
ylab.ind=paste("Frequency (out of ",length(het.ind)," individuals)",sep="")
ylab.snp=paste("Frequency (out of ",length(het.snp)," markers)",sep="")
pdf("GAPIT.Heterozygosity.pdf", width =10, height = 6)
par(mfrow=c(1,2),mar=c(5,5,1,1)+0.1)
hist(het.ind,col="gray", main="",ylab=ylab.ind, xlab="Heterozygosity of individuals")
hist(het.snp,col="gray", main="",ylab=ylab.snp, xlab="Heterozygosity of markers")
dev.off()
rm(X, H, het.ind, het.snp) #Feree memory
myFig21<-myGI
myFig21<-myFig21[!is.na(as.numeric(as.matrix(myFig21[,3]))),]
n<-nrow(myFig21)
maxchr<-0
for(i in 1:n){
if(as.numeric(as.matrix(myFig21[i,2]))>maxchr){
maxchr<-as.numeric(as.matrix(myFig21[i,2]))
}
}
n_end<-maxchr
if(maxchr==0){
chr=0
}
#n_end<-as.numeric(as.matrix(myFig21[n,2]))
aaa<-NULL
for(i in 0:n_end){
#myChr<-myFig21[myFig21[,2]==i,]
myChr<-myFig21[as.numeric(as.matrix(myFig21[,2]))==i,]
index<-order(as.numeric(as.matrix(as.data.frame(myChr[,3]))))
aaa<-rbind(aaa,myChr[index,])
}
myFig2<-aaa
if(is.null(w1_end)){
if(nrow(myFig2[as.numeric(as.matrix(myFig2[,2]))==chr,])>100){
w1_end=100
}else{
w1_end=nrow(myFig2[as.numeric(as.matrix(myFig2[,2]))==chr,])
}
}
subResult<-matrix(0,n,1)
for(i in 1 :( n-1))
{
k<-as.numeric(as.matrix(myFig2[i+1,3]))-as.numeric(as.matrix(myFig2[i,3]))
if(k>0){
subResult[i]<-k
}
else{
subResult[i]<-0
}}
results<-cbind(myFig2,subResult)
#####Out Distribution of SNP density ##########
#####Out Accumulation##########
kk0<-order(as.numeric(as.matrix(results[,4])))
myFig22<-results[kk0,]
m<-nrow(myFig22)
kk1<-matrix(1:m,m,1)
results2<-cbind(myFig22,kk1)
max2<-max(myFig22[,4])
pdf("GAPIT.Marker.Density.pdf", width =10, height = 6)
par(mar=c(5,5,4,5)+0.1)
hist(as.numeric(as.matrix(results[,4])),xlab="Density",main="Distribution of SNP",breaks=12, cex.axis=0.9,col = "dimgray",cex.lab=1.3)###,xlim=c(0,25040359))
par(new=T)
plot(results2[,4],results2[,5]/m,xaxt="n", yaxt="n",bg="lightgray",xlab="",ylab="",type="l",pch=20,col="#990000",cex=1.0,cex.lab=1.3, cex.axis=0.9, lwd=3,las=1,xlim=c(0,max2))
axis(4,col="#990000",col.ticks="#990000",col.axis="#990000")
mtext("Accumulation Frequency",side=4,line=3,font=2,font.axis=1.3,col="#990000")
abline(h=0,col="forestgreen",lty=2)
abline(h=1,col="forestgreen",lty=2)
dev.off()
#####Out Moving Average of density##########
#print(unique(myGI[,2]))
myGD0<-myGD[,as.numeric(myGI[,2])==chr]
gc()
myGM0<-myGI[myGI[,2]==chr,]
##remove invalid SNPs
#X<-myGD0[,-1]
X<-myGD0
colMax=apply(X,2,max)
colMin=apply(X,2,min)
#mono=as.numeric(colMax)-as.numeric(colMin)
mono=colMax-colMin
index=mono<10E-5
X=X[,!index]
myFig3<-myGM0[!index,]
n3<-nrow(myFig3)
kk3<-order(as.numeric(as.matrix(myFig3[,3])))
myFig23<-myFig3[kk3,]
myGD3<-X[,kk3]
##set windows long
##w1_start<-30
##w1_end<-230
###get windows numeric snp at the same chr
#print(w1_start)
#print(w1_end)
#print(dim(myFig3))
if(nrow(myFig23)<w1_end)w1_end=nrow(myFig23)
#print(w1_start)
#print(w1_end)
results3_100<-myFig23[w1_start:w1_end,]
myGD3_100<-myGD3[,w1_start:w1_end]
km<-w1_end-w1_start+1
##get number of Density about snp
sum_number_Density <-0
for(j in 1:km)
{
sum_number_Density<-sum_number_Density+(j-1)
}
save_Density_Cor<-matrix(0.0,sum_number_Density,3)
save_Density_Cor_name<-matrix("",sum_number_Density,1)
countSDC<-1
for(j in 1:(km-1))
{
for(k in (j+1):km)
{
save_Density_Cor[countSDC,1]<-abs(as.numeric(as.matrix(results3_100[k,3]))-as.numeric(as.matrix(results3_100[j,3])))
save_Density_Cor[countSDC,2]<-cor(myGD3_100[,j],myGD3_100[,k])
#options(digits=8)
#save_Density_Cor[countSDC,3]<-as.numeric(as.matrix(format(cor(myGD3_100[,j],myGD3_100[,k])%*% cor(myGD3_100[,j],myGD3_100[,k]),digits=8)))
save_Density_Cor[countSDC,3]<-cor(myGD3_100[,j],myGD3_100[,k])%*% cor(myGD3_100[,j],myGD3_100[,k])
save_Density_Cor_name[countSDC,1]<-paste(results3_100[j,1],"::::",results3_100[k,1],seq="")
countSDC<-countSDC+1
}
}
#result3_30<-as.data.frame(cbind(save_Density_Cor_name,save_Density_Cor))
k3_3<-order(save_Density_Cor[,1])
result3_3<-save_Density_Cor[k3_3,]
##set moving average value
##mav1<-100
result_mav2<-matrix(0.0,sum_number_Density-mav1,1)
mav1_1<-floor(mav1/2)
mav1_1_end<-sum_number_Density-mav1+mav1_1
result_mav1<-result3_3[(mav1_1+1):mav1_1_end,1]
for(g in 1:(sum_number_Density-mav1)){
sum<-0
for(i in g:(g+mav1-1)){
sum<-sum+result3_3[i,3]
}
#result_mav2[g]<-sum/mav1*5
result_mav2[g]<-sum/mav1
}
result_mav<-cbind(result_mav1,result_mav2)
pdf("GAPIT.Marker.LD.pdf", width =10, height = 6)
par(mar = c(5,5,5,5))
plot(as.matrix(result3_3[,1]),as.matrix(result3_3[,3]),bg="dimgray",xlab="Distance",ylab="R Square",pch=1,cex=0.9,cex.lab=1.2, lwd=0.75,las=1)
#,ylim=c(0,round(max(result3_3[,3]))))
lines(result_mav[,2]~result_mav[,1], lwd=6,type="l",pch=20,col="#990000")
dev.off()
print(paste("GAPIT.Genotype.View ", ".Two pdf generate.","successfully!" ,sep = ""))
#GAPIT.Genotype.View
}
#=============================================================================================
`GAPIT.HMP2Num` <-
function(nLines=n,fileHMP="hmp.txt",fileNum="num.txt",bit=1,SNP.effect="Add",SNP.impute="Middle",heading=TRUE, Create.indicator = FALSE, Major.allele.zero = FALSE){
#Object: To convert hmp file to numerical file
#Input: hmp genotype file
#Output: Numerical genotype file
#Authors: Zhiwu Zhang
# Last update: May 23, 2013
##############################################################################################
#print("GAPIT.HMP2Num start")
setwd("/Users/Zhiwu/Dropbox/Current/paper/BigData/BUS/Robust/MaizeGBS")
fileHMP="NAMs26HM2.c10.imp.hmp.txt"
fileNum="NAMs26HM2.c10s.imp.num.txt"
bit=1
SNP.effect="Add"
SNP.impute="Middle"
Major.allele.zero = FALSE
system.time({
n=2000
fileHMPCon<-file(fileHMP, open="r")
#fileNumCon<-file(fileNum, open="r")
tt<-readLines(fileHMPCon, n=1) #header
for(i in 1:n){
if(i %% 100 == 0)print(i)
tt<-readLines(fileHMPCon, n=1)
#tt2<-na.omit(as.numeric(unlist(strsplit(tt, "\t"))))
tt2<-unlist(strsplit(tt, "\t"))
#GM
rs=tt2[1]
chrom=tt2[3]
pos=tt2[4]
#GD
GD= GAPIT.Numericalization(x=tt2[-c(1:11)],bit=bit,effect=SNP.effect,impute=SNP.impute, Major.allele.zero=Major.allele.zero)
#Output
#print(i)
#print(tt2[12:52])
#print(GD[1:41])
#writeLines(tt2, fileNumCon,append=TRUE)
}
close.connection(fileHMPCon)
})
#print("GAPIT.HMP2Num accomplished successfully!")
} #GAPIT.HMP2Num ends here
#=============================================================================================
`GAPIT.HapMap` <-
function(G,SNP.effect="Add",SNP.impute="Middle",heading=TRUE, Create.indicator = FALSE, Major.allele.zero = FALSE){
#Object: To convert character SNP genotpe to numerical
#Output: Coresponding numerical value
#Authors: Feng Tian and Zhiwu Zhang
# Last update: May 30, 2011
##############################################################################################
print(paste("Converting HapMap format to numerical under model of ", SNP.impute,sep=""))
#gc()
#GAPIT.Memory.Object(name.of.trait="HapMap.Start")
#GT=data.frame(G[1,-(1:11)])
if(heading){
GT= t(G[1,-(1:11)])
GI= G[-1,c(1,3,4)]
}else{
GT=NULL
GI= G[,c(1,3,4)]
}
#Set column names
if(heading)colnames(GT)="taxa"
colnames(GI)=c("SNP","Chromosome","Position")
#Initial GD
GD=NULL
bit=nchar(as.character(G[2,12])) #to determine number of bits of genotype
#print(paste("Number of bits for genotype: ", bit))
print("Perform numericalization")
if(heading){
if(!Create.indicator) GD= apply(G[-1,-(1:11)],1,function(one) GAPIT.Numericalization(one,bit=bit,effect=SNP.effect,impute=SNP.impute, Major.allele.zero=Major.allele.zero))
if(Create.indicator) GD= t(G[-1,-(1:11)])
}else{
if(!Create.indicator) GD= apply(G[ ,-(1:11)],1,function(one) GAPIT.Numericalization(one,bit=bit,effect=SNP.effect,impute=SNP.impute, Major.allele.zero=Major.allele.zero))
if(Create.indicator) GD= t(G[ ,-(1:11)])
}
#set GT and GI to NULL in case of null GD
if(is.null(GD)){
GT=NULL
GI=NULL
}
#print("The dimension of GD is:")
#print(dim(GD))
if(!Create.indicator) {print(paste("Succesfuly finished converting HapMap which has bits of ", bit,sep="")) }
return(list(GT=GT,GD=GD,GI=GI))
}#end of GAPIT.HapMap function
#=============================================================================================
`GAPIT.IC` <-
function(DP=NULL){
#Object: To Intermediate Components
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("GAPIT.IC in process...")
Y=DP$Y
PC=DP$PC
CV=DP$CV
GD=DP$GD
noCV=FALSE
if(is.null(CV)){
noCV=TRUE
CV=Y[,1:2]
CV[,2]=1
colnames(CV)=c("taxa","overall")
print(paste("There is 0 Covarinces.",sep=""))
}
taxa_Y=as.character(Y[,1])
taxa_GD=as.character(GD[,1])
if(DP$PCA.total>0&!is.null(DP$CV))CV=GAPIT.CVMergePC(DP$CV,PC)
if(DP$PCA.total>0&is.null(DP$CV))CV=PC
taxa_comGD=as.character(GD[,1])
taxa_comY=as.character(Y[,1])
taxa_CV=as.character(CV[,1])
taxa_comall=intersect(intersect(taxa_comGD,taxa_comY),taxa_CV)
comCV=CV[taxa_CV%in%taxa_comall,]
comGD=GD[taxa_comGD%in%taxa_comall,]
comY=Y[taxa_comY%in%taxa_comall,]
GT=as.matrix(as.character(taxa_comall))
print(paste("There are ",length(GT)," common individuals in genotype , phenotype and CV files.",sep=""))
if(nrow(comCV)!=length(GT))stop ("GAPIT says: The number of individuals in CV does not match to the number of individuals in genotype files.")
print("The dimension of total CV is ")
print(dim(comCV))
print("GAPIT.IC accomplished successfully for multiple traits. Results are saved")
if(DP$kinship.algorithm%in%c("FarmCPU","Blink","MLMM")){
return (list(Y=comY,GT=GT,PCA=comCV,K=DP$KI,GD=comGD,GM=DP$GM,myallCV=CV,myallGD=GD))
}else{
return (list(Y=comY,GT=GT,PCA=comCV,K=DP$KI,GD=comGD,GM=DP$GM,myallCV=CV,myallGD=GD,myallY=Y))
}
} #end of GAPIT IC function
#=============================================================================================
`GAPIT.ID` <-
function(DP=NULL,IC=NULL,SS=NULL,RS=NULL,cutOff=0.01,
DPP=100000,Create.indicator=FALSE,
FDR.Rate = 1,QTN.position=NULL,plot.style="Oceanic",
file.output=TRUE,SNP.MAF=0,CG=NULL,plot.bin=10^9 ){
#Object: To Interpretation and Diagnoses
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("GAPIT.ID in process...")
#Define the funcitno here
if(is.null(DP)&is.null(IC))#inputdata is other method result
{
GWAS=RS
GI=RS[,1:3]
GI=GI[order(GI[,2]),]
GI=GI[order(GI[,1]),]
#print(QTN.position)
ps=RS[,4]
nobs=nrow(RS)
if(ncol(RS)>4)
{maf=RS[,5]
maf_pass=TRUE
}
if(ncol(RS)<5)
{maf_pass=FALSE
maf=0.5
}
rsquare_base=rep(NA,length(ps))
rsquare=rep(NA,length(ps))
df=rep(NA,length(nobs))
tvalue=rep(NA,length(nobs))
stderr=rep(NA,length(nobs))
effect.est=rep(NA,length(nobs))
if(is.na(maf[1])) maf=matrix(.5,nrow(GWAS),1)
print("Filtering SNPs with MAF..." )
index=maf>=SNP.MAF
PWI.Filtered=cbind(GI,ps,maf,nobs,rsquare_base,rsquare)#[index,]
colnames(PWI.Filtered)=c("SNP","Chromosome","Position ","P.value", "maf", "nobs", "Rsquare.of.Model.without.SNP","Rsquare.of.Model.with.SNP")
if(!is.null(PWI.Filtered))
{
print("Calculating FDR..." )
PWIP <- GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure(PWI = PWI.Filtered, FDR.Rate = FDR.Rate, FDR.Procedure = "BH")
print("QQ plot..." )
if(file.output) GAPIT.QQ(P.values = ps, name.of.trait = name.of.trait,DPP=DPP)
print("Manhattan plot (Genomewise)..." )
if(file.output) GAPIT.Manhattan(GI.MP = cbind(GI[,-1],ps), name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff,seqQTN=QTN.position,plot.style=plot.style,plot.bin=plot.bin)
print("Manhattan plot (Chromosomewise)..." )
#if(file.output) GAPIT.Manhattan(GI.MP = PWIP$PWIP[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Chromosomewise",cutOff=cutOff)
if(file.output) GAPIT.Manhattan(GI.MP = cbind(GI[,-1],ps), name.of.trait = name.of.trait, DPP=DPP, plot.type = "Chromosomewise",cutOff=cutOff,plot.bin=plot.bin)
#Association Table
print("Association table..." )
#GAPIT.Table(final.table = PWIP$PWIP, name.of.trait = name.of.trait,SNP.FDR=SNP.FDR)
# GWAS=PWIP$PWIP[PWIP$PWIP[,9]<=DP$SNP.FDR,]
# print(head(GWAS))
print("Joining tvalue and stderr" )
DTS=cbind(GI,df,tvalue,stderr,effect.est)
colnames(DTS)=c("SNP","Chromosome","Position","DF","t Value","std Error","effect")
print("Creating ROC table and plot" )
if(file.output) myROC=GAPIT.ROC(t=tvalue,se=stderr,Vp=var(ys),trait=name.of.trait)
print("ROC table and plot created" )
print("MAF plot..." )
if(file.output&maf_pass) myMAF1=GAPIT.MAF(MAF=maf,P=ps,E=NULL,trait=name.of.trait)
if(file.output){
write.table(GWAS, paste("GAPIT.", name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
write.table(DTS, paste("GAPIT.", name.of.trait, ".Df.tValue.StdErr.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#if(!byPass) write.table(GWAS.2, paste("GAPIT.", name.of.trait, ".Allelic_Effect_Estimates.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}#end file.output
}#end DP
}else{ #inputdata is GAPIT3 result
name.of.trait=DP$memo
GWAS=SS$GWAS
#print(head(GWAS))
Pred=SS$Pred
GI=GWAS
GI=GI[order(GI[,3]),]
GI=GI[order(GI[,2]),]
byPass=TRUE
if(DP$kinship.algorithm%in%c("FarmCPU","MLMM","Blink"))byPass=FALSE
if(byPass)
{
# print(head(SS$GWAS))
ps=SS$TV$ps
nobs=SS$TV$nobs
maf=GWAS$maf
#maf=SS$TV$maf
rsquare_base=SS$TV$rsquare_base
rsquare=SS$TV$rsquare
df=SS$TV$df
tvalue=SS$TV$tvalue
stderr=SS$TV$stderr
effect.est=SS$mc
effect=SS$mc
#GI=cbind(GI,effect)
if(DP$file.output&!is.null(SS$Compression)&!is.na(SS$Compression[1,6])) GAPIT.Compression.Visualization(Compression = SS$Compression, name.of.trait = DP$name.of.trait)
}else{
maf=GI$maf
ps=GI$P.value
nobs=GI$nobs
rsquare_base=rep(NA,length(ps))
rsquare=rep(NA,length(ps))
df=rep(NA,length(nobs))
tvalue=rep(NA,length(nobs))
stderr=rep(NA,length(nobs))
effect.est=GI$effect
}
if(is.na(maf[1])) maf=matrix(.5,nrow(GI),1)
if(!is.null(IC$GD)&DP$SNP.test)
{
print("Filtering SNPs with MAF..." )
#index=maf>=DP$SNP.MAF
#PWI.Filtered=cbind(GI[,-5],rsquare_base,rsquare)
PWI.Filtered=cbind(GWAS[,1:6],rsquare_base,rsquare)
colnames(PWI.Filtered)=c("SNP","Chromosome","Position ","P.value", "maf", "nobs", "Rsquare.of.Model.without.SNP","Rsquare.of.Model.with.SNP")
if(!is.null(PWI.Filtered))
{
#Run the BH multiple correction procedure of the results
#Create PWIP, which is a table of SNP Names, Chromosome, bp Position, Raw P-values, FDR Adjusted P-values
print("Calculating FDR..." )
PWIP <- GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure(PWI = PWI.Filtered, FDR.Rate = FDR.Rate, FDR.Procedure = "BH")
#print(str(PWIP))
print("QQ plot..." )
if(DP$file.output) GAPIT.QQ(P.values = GI$P.value, name.of.trait = DP$name.of.trait,DPP=DP$DPP)
print("Manhattan plot (Genomewise)..." )
if(DP$file.output) GAPIT.Manhattan(GI.MP = GWAS[,2:4], name.of.trait = DP$name.of.trait, DPP=DP$DPP, plot.type = "Genomewise",cutOff=DP$cutOff,seqQTN=DP$QTN.position,plot.style=DP$plot.style,plot.bin=DP$plot.bin,chor_taxa=DP$chor_taxa)
#print("@@@@@@@@@@@@@@@@@@@@@@@@")
print("Manhattan plot (Chromosomewise)..." )
if(DP$file.output) GAPIT.Manhattan(GI.MP = GWAS[,2:4],GD=IC$GD[,-1], CG=DP$CG,name.of.trait = DP$name.of.trait, DPP=DP$DPP, plot.type = "Chromosomewise",cutOff=DP$cutOff,plot.bin=DP$plot.bin)
#Association Table
print("Association table..." )
print("Joining tvalue and stderr" )
# print(head(GWAS))
# print(length(df))
# print(length(tvalue))
# print(length(stderr))
# print(length(effect.est))
DTS=cbind(GWAS[,1:3],df,tvalue,stderr,effect.est)
colnames(DTS)=c("SNP","Chromosome","Position","DF","t Value","std Error","effect")
print("Creating ROC table and plot" )
if(DP$file.output) myROC=GAPIT.ROC(t=tvalue,se=stderr,Vp=var(as.matrix(DP$Y[,2])),trait=DP$name.of.trait)
print("ROC table and plot created" )
print("MAF plot..." )
if(DP$file.output) myMAF1=GAPIT.MAF(MAF=maf,P=ps,E=NULL,trait=DP$name.of.trait)
print("GAPIT.Interactive.Manhattan")
print(DP$Inter.type)
#GI=GI[order(GI[,4]),]
#print(head(GI))
if(ncol(GI)>1)
{new_GI=merge(PWIP$PWIP,GI[,c("SNP","effect")],by.x="SNP",by.y="SNP")
}else{
new_GI=GI
}
new_GI=new_GI[order(new_GI[,4]),]
#print(head(new_GI))
if(DP$file.output&DP$Inter.Plot) GAPIT.Interactive.Manhattan(GWAS=new_GI,X_fre=maf,plot.type=DP$Inter.type,name.of.trait = DP$name.of.trait)
if(DP$file.output){
write.table(new_GI, paste("GAPIT.", DP$name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
write.table(DTS, paste("GAPIT.", DP$name.of.trait, ".Df.tValue.StdErr.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#print(head(GWAS.2))
#if(byPass) write.table(GWAS.2[,1:4], paste("GAPIT.", DP$name.of.trait, ".Allelic_Effect_Estimates.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}#end file.output
}#PWI.Filtered
}#end IC$GD)
print("GAPIT.ID accomplished successfully for multiple traits. Results are saved")
return ()
}#is.null(DP)&is.null(IC)
} #end of GAPIT.ID function
#=============================================================================================
`GAPIT.Imputation` <-
function(x,GI=NULL,impute="Middle",byRow=TRUE){
#Object: To impute NA in genome
#Output: Coresponding numerical value
#Authors: Zhiwu Zhang
#Writer: Jiabo Wang
# Last update: April 13, 2016
##############################################################################################
n=length(x)
lev=levels(as.factor(x))
lev=setdiff(lev,NA)
#print(lev)
len=length(lev)
count=1:len
for(i in 1:len){
count[i]=length(x[(x==lev[i])])
}
position=order(count)
#print(position)
if(impute=="Middle") {x[is.na(x)]=1 }
if(len==3){
if(impute=="Minor") {x[is.na(x)]=position[1] -1}
if(impute=="Major") {x[is.na(x)]=position[len]-1}
}else{
if(impute=="Minor") {x[is.na(x)]=2*(position[1] -1)}
if(impute=="Major") {x[is.na(x)]=2*(position[len]-1)}
}
if(byRow) {
result=matrix(x,n,1)
}else{
result=matrix(x,1,n)
}
return(result)
}#end of GAPIT.Numericalization function
#=============================================================================================
`GAPIT.Interactive.GS`<-
function(model_store=NULL,Y=NULL,myGD=NULL,myGM=NULL,myKI=NULL,myY=NULL,myCV=NULL,rel=NULL,h2=NULL,NQTN=NULL
)
#model_store is the store of all model names
#Y is the real phenotype
#
{
# e=20
# #NQTN=100
# #h2=0.25
# taxa=as.character(myGD[,1])
# myY=Y0[Y0[,1]%in%taxa,c(1,e)]
# myGD=myGD[taxa%in%myY[,1],]
# nfold=5
# repli=1
# sets=sample(cut(1:nrow(myY ),nfold,labels=FALSE),nrow(myY ))
# j=1
# training=myY
# training[sets==j,2]=NA
# training_index=is.na(training[,2])
# testing=myY[training_index,]
# cblup_gapit=GAPIT(Y=training,CV=PC,PCA.total=0,KI=myKI,group.from=200,group.to=2000,group.by=600,SNP.test=F,file.output=F)
# gblup_gapit=GAPIT(Y=training,CV=PC,PCA.total=0,KI=myKI,group.from=2000,group.to=2000,group.by=100,SNP.test=F,file.output=F)
# sblup_gapit=GAPIT(Y=training,CV=PC,PCA.total=0,GD=myGD,GM=myGM,group.from=2000,SUPER_GS=TRUE,sangwich.top="MLM",sangwich.bottom="SUPER",LD=0.1,SNP.test=F,file.output=F,inclosure.from=200,inclosure.to=1000,inclosure.by=200,bin.from=10000,bin.to=100000,bin.by=10000)
# cblup_pred=cblup_gapit$Pred[training_index,]
# gblup_pred=gblup_gapit$Pred[training_index,]
# sblup_pred=sblup_gapit$Pred[training_index,]
# testing_index=!is.na(testing[,2])
# gblup_r_once=cor(testing[testing_index,2],gblup_pred[testing_index,8])
# cblup_r_once=cor(testing[testing_index,2],cblup_pred[testing_index,8])
# sblup_r_once=cor(testing[testing_index,2],sblup_pred[testing_index,8])
# result=cbind(testing[testing_index,],gblup_pred[testing_index,8],cblup_pred[testing_index,8],sblup_pred[testing_index,8])
# colnames(result)=c("taxa","observed","gBLUP","cBLUP","sBLUP")
# gblup_r_once
# cblup_r_once
# sblup_r_once
# write.table(result,paste("gcs_",e,".txt",sep=""))
myY=read.table(paste("gcs_",e,".txt",sep=""),head=T)
Observed=myY$observed
Predicted=myY$gBLUP
if(!require(plotly)) install.packages("plotly")
library(plotly)
p <- plot_ly(
type = 'scatter',
x = ~Observed,
y = ~Predicted,
data=myY,
text = ~paste("Taxa: ",taxa,"<br>Observed: ",round(observed,4) , '<br>gBLUP:', round(gBLUP,4)),
#size=2*y/max(y),
color = I("red"),
name=c("gBLUP")
)%>%add_trace(
type = 'scatter',
x = ~observed,
y = ~cBLUP,
#data=myY,
text = ~paste("Taxa: ",taxa,"<br>Observed: ",round(observed,4) , '<br>cBLUP:', round(cBLUP,4)),
#size=2*y/max(y),
color = I("blue"),
name=c("cBLUP")
)%>%add_trace(
type = 'scatter',
x = ~observed,
y = ~sBLUP,
#data=myY,
text = ~paste("Taxa: ",taxa,"<br>Observed: ",round(observed,4) , '<br>sBLUP:', round(sBLUP,4)),
#size=2*y/max(y),
color = I("green"),
name=c("sBLUP")
)
htmltools::save_html(p, "Interactive.GS.html")
}
`GAPIT.Interactive.Manhattan`<-
function(GWAS=NULL,MAF.threshold=seq(0,0.5,.1),cutOff=0.01,DPP=50000,X_fre=NULL,plot.type=c("m","q"),name.of.trait = "Trait"
)
{
if(is.null(GWAS)) stop("Please add GWAS result in here!!!")
MP=GWAS[,2:4]
#print(head(GWAS))
GWAS=GWAS[order(GWAS[,3]),]
GWAS=GWAS[order(GWAS[,2]),]
#print(GWAS[GWAS[,4]==min(GWAS[,4]),2])
taxa=as.character(GWAS[,1])
numMarker=nrow(GWAS)
bonferroniCutOff01=-log10(0.01/numMarker)
bonferroniCutOff05=-log10(0.05/numMarker)
# deal with P value to log
Ps=as.numeric(as.vector(GWAS[,4]))
logPs <- -log10(Ps)
logPs[is.na(logPs)]=0
y.lim <- ceiling(max(GWAS[,4]))
chrom_total=as.numeric(as.character((GWAS[,2])))
#print(GWAS[GWAS[,4]==min(GWAS[,4]),])
#print("!!!!")
#print(chrom_total[logPs==max(logPs)])
POS=as.numeric(as.vector(GWAS[,3]))
#print(head(POS))
chm.to.analyze <- as.numeric(as.character(unique(GWAS[,2])))
chm.to.analyze=chm.to.analyze[order(as.numeric(as.character(chm.to.analyze)))]
#chm.to.analyze = factor(sort(chm.to.analyze))
numCHR= length(chm.to.analyze)
print(chm.to.analyze)
ticks=NULL
lastbase=0
#change base position to accumulatives (ticks)
for (i in chm.to.analyze)
{
index=(chrom_total==i)
ticks <- c(ticks, lastbase+mean(POS[index]))
POS[index]=POS[index]+lastbase
lastbase=max(POS[index])
}
x0 <- POS
y0 <- as.numeric(logPs)
z0 <- chrom_total
posi0<-as.numeric(as.vector(GWAS$Position))
maf0 <- as.numeric(as.vector(GWAS$maf))
effect0<- as.numeric(as.vector(GWAS$effect))
#print(head(z0))
position=order(y0,decreasing = TRUE)
index0=GAPIT.Pruning(y0[position],DPP=DPP)
index=position[index0]
#order by P value
x=x0[index]
y=y0[index]
z=z0[index]
taxa=taxa[index]
posi=posi0[index]
maf=maf0[index]
effect=effect0[index]
plot.color=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(numCHR/5))
if(c("m")%in%plot.type)
{
Position=x
P_value=y
z[z<10]=paste("0",z[z<10],sep="")
zz=paste("Chr_",z,sep="")
#print(zz)
if(!require(plotly)) install.packages("plotly")
#print("!!!!!")
#print(head(Position))
library(plotly)
p <- plot_ly(
type = 'scatter',
x = ~Position,
y = ~P_value,
colorscale='Viridis',
reversescale =T,
#symbol="circle",
text = ~paste("SNP: ", taxa, "<br>Posi: ", posi,"<br>MAF: ", round(maf,2),"<br>Effect: ",round(effect,2)),
color = ~as.character(zz)
)%>%
add_trace(y=bonferroniCutOff01,name = 'CutOff-0.01',color=I("red"),mode="line",width=1.4,text="")%>%
add_trace(y=bonferroniCutOff05,name = 'CutOff-0.05',color=I("red"),mode="line",line=list(width=1.4,dash='dot'),text="")%>%
layout(title = "Interactive.Manhattan.Plot",
#showticklabels = FALSE,
#legend = list(orientation = 'h'),
xaxis = list(title = "Chromsome",zeroline = FALSE,showticklabels = FALSE),
yaxis = list (title = "-Log10(p)"))
htmltools::save_html(p, paste("Interactive.Manhattan.",name.of.trait,".html",sep=""))
}
################ for QQ plot
if(c("q")%in%plot.type)
{
P.values=y
p_value_quantiles <- (1:length(P.values))/(length(P.values)+1)
log.P.values <- P.values
log.Quantiles <- -log10(p_value_quantiles)
index=GAPIT.Pruning(log.P.values,DPP=DPP)
log.P.values=log.P.values[index ]
log.Quantiles=log.Quantiles[index]
N=length(P.values)
N1=length(log.Quantiles)
## create the confidence intervals
c95 <- rep(NA,N1)
c05 <- rep(NA,N1)
for(j in 1:N1){
i=ceiling((10^-log.Quantiles[j])*N)
if(i==0)i=1
c95[j] <- qbeta(0.95,i,N-i+1)
c05[j] <- qbeta(0.05,i,N-i+1)
#print(c(j,i,c95[j],c05[j]))
}
#CI shade
#plot3d(NULL, xlim = c(0,max(log.Quantiles)), zlim = c(0,max(log.P.values)), type="l",lty=5, lwd = 2, axes=FALSE, xlab="", ylab="",col="gray")
index=length(c95):1
zz=paste("Chr_",z,sep="")
Expected=log.Quantiles
Observed=log.P.values
#abline(a = 0, b = 1, col = "red",lwd=2)
qp <- plot_ly(
type = 'scatter',
x = ~Expected,
y = ~Observed,
text = ~paste("SNP: ", taxa,"<br>Chr: ",zz,"<br>Posi: ", posi, "<br>MAF: ", round(maf,2),"<br>Effect: ",round(effect,2)),
#size=2*y/max(y),
name = "SNP",
opacity=0.5,
)%>%add_lines(x=log.Quantiles,y=log.Quantiles,color=I("red"),
mode = 'lines',name="Diag",text="")%>%
layout(title = "Interactive.QQ.Plot",
xaxis = list(title = "Expected -Log10(p)"),
yaxis = list (title = "Observed -Log10(p)"),
#showticklabels = FALSE,
showlegend = FALSE)
htmltools::save_html(qp, paste("Interactive.QQ ",name.of.trait,".html",sep=""))
}
print("GAPIT.Interactive.Plot has done !!!")
}#end of GAPIT.Interactive.Manhattan
#=============================================================================================
`GAPIT.Judge`<-
function(Y=Y,G=NULL,GD=NULL,KI=NULL,GM=NULL,group.to=group.to,group.from=group.from,sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,kinship.algorithm=kinship.algorithm,PCA.total=PCA.total,model="MLM",SNP.test=TRUE){
#Object: To judge Pheno and Geno data practicability
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("--------------------Phenotype and Genotype ----------------------------------")
if(ncol(Y)<2) stop ("Phenotype should have taxa name and one trait at least. Please correct phenotype file!")
print(kinship.algorithm)
if(is.null(KI)&is.null(GD) & kinship.algorithm!="SUPER"&is.null(G)) stop ("GAPIT says: Kinship is required. As genotype is not provided, kinship can not be created.")
if(kinship.algorithm=="FarmCPU"&SNP.test==FALSE)stop("FarmCPU is only for GWAS, plase set: SNP.test= TRUE")
#if((!is.null(GD))&(!is.null(G))) stop("GAPIT Says:Please put in only one type of geno data.")
if(is.null(GD)&is.null(G)&is.null(KI))stop ("GAPIT Says:GAPIT need genotype!!!")
if(!is.null(GD) & is.null(GM) & (is.null(G)) &SNP.test) stop("GAPIT Says: Genotype data and map files should be in pair")
if(is.null(GD) & !is.null(GM) & (is.null(G)) &SNP.test) stop("GAPIT Says: Genotype data and map files should be in pair")
if (is.null(GD[,1]%in%Y[,1])|is.null(colnames(G)[-c(1:11)]%in%Y[,1]))stop("GAPIT Says: There are no common taxa between genotype and phenotype")
if (!is.null(Y)) nY=nrow(Y)
if (!is.null(Y)) ntrait=ncol(Y)-1
print(paste("There are ",ntrait," traits in phenotype data."))
print(paste("There are ",nY," individuals in phenotype data."))
if (!is.null(G)) nG=nrow(G)-11
if (!is.null(GD))
{nG=ncol(GD)-1
print(paste("There are ",nG," markers in genotype data."))}
print("Phenotype and Genotype are test OK !!")
print("--------------------GAPIT Logical ----------------------------------")
#if (group.to>nY&is.null(KI))group.to=nY
#if (group.from>group.to&is.null(KI)) group.from=group.to
if(!is.null(sangwich.top) & is.null(sangwich.bottom) ) stop("GAPIT Says: SUPER method need sangwich.top and bottom")
if(is.null(sangwich.top) & !is.null(sangwich.bottom) ) stop("GAPIT Says: SUPER method need sangwich.top and bottom")
if(kinship.algorithm=="Separation"&PCA.total==0) stop ("GAPIT Says: Separation kinship need PCA.total>0")
return (list(group.to=group.to,group.from=group.from))
}#end of GAPIT.Pheno.Geno.judge function
#=============================================================================================
`GAPIT.Liner` <-
function(Y,GD,CV){
#Object: To have Y, GD and CV the same size and order
#Input: Y,GDP,GM,CV
#Input: GD - n by m +1 dataframe or n by m big.matrix
#Input: GDP - n by m matrix. This is Genotype Data Pure (GDP). THERE IS NOT COLUMN FOR TAXA.
#Input: orientation-Marker in GDP go colmun or row wise
#Requirement: Y, GDP and CV have same taxa order. GDP and GM have the same order on SNP
#Output: GWAS,GPS,Pred
#Authors: Zhiwu Zhang
# Last update: Febuary 24, 2013
##############################################################################################
#print("GAPIT.Liner Started")
#print(date())
#print("Memory used at begining of BUS")
#print(memory.size())
#print("dimension of Y,GD and CV at begining")
#print(dim(Y))
#print(dim(GD))
#print(dim(CV))
if(!is.null(CV))taxa=intersect(intersect(GD[,1],Y[,1]),CV[,1])
if(is.null(CV))taxa=intersect(GD[,1],Y[,1])
Y=Y[match(taxa, Y[,1], nomatch = 0),]
GD=GD[match(taxa, GD[,1], nomatch = 0),]
if(!is.null(CV)) CV=CV[match(taxa, CV[,1], nomatch = 0),]
Y = Y[order(Y[,1]),]
GD = GD[order(GD[,1]),]
if(!is.null(CV)) CV = CV[order(CV[,1]),]
#print("dimension of Y,GD and CV at end")
#print(dim(Y))
#print(dim(GD))
#print(dim(CV))
print("GAPIT.Liner accomplished successfully")
return (list(Y=Y,GD=GD,CV=CV))
}#The function GAPIT.Liner ends here
#=============================================================================================
`GAPIT.Log` <-
function(Y=Y,KI=KI,Z=Z,CV=CV,SNP.P3D=SNP.P3D,
group.from = group.from ,group.to =group.to ,group.by = group.by ,kinship.cluster = kinship.cluster, kinship.group= kinship.group,
ngrid = ngrid , llin = llin , ulim = ulim , esp = esp ,name.of.trait = name.of.trait){
#Object: To report model factors
#Output: Text file (GAPIT.Log.txt)
#Authors: Zhiwu Zhang
# Last update: may 16, 2011
##############################################################################################
#Creat storage
facto <- list(NULL)
value <- list(NULL)
#collecting model factors
facto[[1]]="Trait"
value[[1]]=paste(dim(Y))
facto[[2]]="group.by "
value[[2]]=group.by
facto[[3]]="Trait name "
value[[3]]=name.of.trait
facto[[4]]="Kinship"
value[[4]]=dim(KI)
facto[[5]]="Z Matrix"
value[[5]]=dim(Z)
facto[[6]]="Covariate"
value[[6]]=dim(CV)
facto[[7]]="SNP.P3D"
value[[7]]=SNP.P3D
facto[[8]]="Clustering algorithms"
value[[8]]=kinship.cluster
facto[[9]]="Group kinship"
value[[9]]=kinship.group
facto[[10]]="group.from "
value[[10]]=group.from
facto[[11]]="group.to "
value[[11]]=group.to
theLog=as.matrix(cbind(facto,value))
#theLog=as.character(as.matrix(cbind(facto,value)))
colnames(theLog)=c("Model", "Value")
file=paste("GAPIT.", name.of.trait,".Log.csv" ,sep = "")
write.table(theLog, file, quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
return (theLog)
}
#=============================================================================================
`GAPIT.MAF` <-
function(MAF=NULL,P=NULL,E=NULL,trait="",threshold.output=.1,plot.style="rainbow"){
#Object: To display probability and effect over MAF
#Input: MAF vector of MAF
#Input: P vector of P values
#Output: A table and plot
#Requirment: NA
#Authors: Zhiwu Zhang
# Start date: April 5, 2013
# Last update: Oct 27, 2015 by Jiabo Wang add notice for P<0.1 is empty
##############################################################################################
#print("MAF plot started")
#print(threshold.output)
#Remove NAs and under threshold
index= which(P<threshold.output & !is.na(MAF))
MAF=MAF[index]
#E=E[index]
P=P[index]
LP=-log10(P)
LPC=round(LP*10,digits = 0)+20
ncolors=max(LPC,na.rm=T)
if(ncolors > 1024) {ncolors=1024}
if(ncolors==-Inf)
{
print("There are no significant gene by this method(<0.1)")
}else{
#print("MAF plot started 0001")
#print(length(P))
#print(ncolors)
#palette(rainbow(ncolors))
#palette(gray(seq(.9,0,len = ncolors)))
#print("MAF plot started 0001b")
pdf(paste("GAPIT.", trait,".MAF.pdf" ,sep = ""), width = 5,height=5)
par(mar = c(5,6,5,3))
theColor=heat.colors(ncolors, alpha = 1)
palette(rev(theColor))
plot(MAF,LP,type="p",lty = 1,lwd=2,col=LPC,xlab="MAF",ylab =expression(Probability~~-log[10](italic(p))),main = trait, cex.axis=1.1, cex.lab=1.3)
#for(i in 2:nc){
#lines(power[,i]~FDR, lwd=2,type="o",pch=i,col=i)
#}
#legend("bottomright", colnames(power), pch = c(1:nc), lty = c(1,2),col=c(1:nc))
palette("default") # reset back to the default
dev.off()
}
} #GAPIT.MAF ends here
#=============================================================================================
`GAPIT.Main` <-
function(Y,G=NULL,GD=NULL,GM=NULL,KI=NULL,Z=NULL,CV=NULL,CV.Inheritance=NULL,SNP.P3D=TRUE,GP=NULL,GK=NULL,
group.from=1000000 ,group.to=1,group.by=10,kinship.cluster="average", kinship.group='Mean',kinship.algorithm=NULL,DPP=50000,
ngrid = 100, llin = -10, ulim = 10, esp = 1e-10,GAPIT3.output=TRUE,
file.path=NULL,file.from=NULL, file.to=NULL, file.total=NULL, file.fragment = 512, file.G=NULL, file.Ext.G=NULL,file.GD=NULL, file.GM=NULL, file.Ext.GD=NULL,file.Ext.GM=NULL,
SNP.MAF=0,FDR.Rate=1,SNP.FDR=1,SNP.effect="Add",SNP.impute="Middle",PCA.total=0, GAPIT.Version=GAPIT.Version,
name.of.trait, GT = NULL, SNP.fraction = 1, seed = 123, BINS = 20,SNP.test=TRUE,SNP.robust="FaST",
LD.chromosome=NULL,LD.location=NULL,LD.range=NULL,model=model,
bin.from=10000,bin.to=5000000,bin.by=1000,inclosure.from=10,inclosure.to=1000,inclosure.by=10,
SNP.permutation=FALSE,SNP.CV=NULL,NJtree.group=NJtree.group,NJtree.type=NJtree.type,plot.bin=plot.bin,
genoFormat=NULL,hasGenotype=NULL,byFile=NULL,fullGD=NULL,PC=NULL,GI=NULL, Timmer = NULL, Memory = NULL,
sangwich.top=NULL,sangwich.bottom=NULL,QC=TRUE,GTindex=NULL,LD=0.05,
file.output=TRUE,cutOff=0.05, Model.selection = FALSE, Create.indicator = FALSE,
QTN=NULL, QTN.round=1,QTN.limit=0, QTN.update=TRUE, QTN.method="Penalty", Major.allele.zero = FALSE,
QTN.position=NULL,SUPER_GD=NULL,SUPER_GS=SUPER_GS,plot.style="Beach",CG=CG,chor_taxa=chor_taxa){
#Object: To perform GWAS and GPS (Genomic Prediction or Selection)
#Output: GWAS table (text file), QQ plot (PDF), Manhattan plot (PDF), genomic prediction (text file), and
# genetic and residual variance components
#Authors: Zhiwu Zhang
# Last update: Oct 23, 2015 by Jiabo Wang add REML threshold and SUPER GD KI
##############################################################################################
#Initial p3d and h2.opt temporaryly
h2.opt=NULL
p3d=list(
ps=NULL,
REMLs=NULL,
stats=NULL,
effect.est=NULL,
rsquare_base=NULL,
rsquare=NULL,
dfs=NULL,
df=NULL,
tvalue=NULL,
stderr=NULL,
maf=NULL,
nobs=NULL,
Timmer=NULL,
Memory=NULL,
vgs=NULL,
ves=NULL,
BLUP=NULL,
BLUP_Plus_Mean=NULL,
PEV=NULL,
BLUE=NULL,
logLM=NULL,
effect.snp=NULL,
effect.cv=NULL
)
if (SUPER_GS)
{
Compression=NULL
kinship.optimum=NULL
kinship=NULL
PC=PC
REMLs=NULL
GWAS=NULL
QTN=NULL
Timmer=GAPIT.Timmer(Infor="GAPIT.SUPER.GS")
Memory=GAPIT.Memory(Infor="GAPIT.SUPER.GS")
#print(model)
SUPER_GS_GAPIT=GAPIT.SUPER.GS(Y=Y,G=G,GD=GD,GM=GM,KI=KI,Z=Z,CV=CV,GK=GK,kinship.algorithm=kinship.algorithm,
bin.from=bin.from,bin.to=bin.to,bin.by=bin.by,inclosure.from=inclosure.from,inclosure.to=inclosure.to,inclosure.by=inclosure.by,
group.from=group.from,group.to=group.to,group.by=group.by,kinship.cluster=kinship.cluster,kinship.group=kinship.group,name.of.trait=traitname,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF= SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,PCA.total=PCA.total,GAPIT.Version=GAPIT.Version,
GT=GT, SNP.fraction = SNP.fraction, seed = seed, BINS = BINS,SNP.test=SNP.test,DPP=DPP, SNP.permutation=SNP.permutation,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,SNP.CV=SNP.CV,SNP.robust=SNP.robust,model=model,
genoFormat=genoFormat,hasGenotype=hasGenotype,byFile=byFile,fullGD=fullGD,PC=PC,GI=GI,Timmer = Timmer, Memory = Memory,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,QC=QC,GTindex=GTindex,LD=LD,file.output=file.output,cutOff=cutOff
)
print("SUPER_GS_GAPIT FUNCTION DONE")
return (list(Compression=SUPER_GS_GAPIT$Compression,kinship.optimum=SUPER_GS_GAPIT$SUPER_kinship,kinship=SUPER_GS_GAPIT$kinship, PC=SUPER_GS_GAPIT$PC,GWAS=GWAS, GPS=SUPER_GS_GAPIT$GPS,Pred=SUPER_GS_GAPIT$Pred,Timmer=Timmer,Memory=Memory,SUPER_GD=SUPER_GS_GAPIT$SUPER_GD,GWAS=NULL,QTN=NULL))
}else{
#print("@@@@@@@")
#print(group.from)
#Handler of SNP.test=F
#Iniciate with two by seven NA matrix
#The seventh is for p values of SNP
DTS=rbind(rep(NA,7),rep(NA,7) )
#End imediatly in one of these situtiona
shortcut=FALSE
LL.save=1e10
#In case of null Y and null GP, sent back genotype only
thisY=Y[,2]
thisY=thisY[!is.na(thisY)]
if(length(thisY) <3){
shortcut=TRUE
}else{
if(var(thisY) ==0) shortcut=TRUE
}
if(shortcut){
print(paste("Y is empty. No GWAS/GS performed for ",name.of.trait,sep=""))
return (list(compression=NULL,kinship.optimum=NULL, kinship=KI,PC=PC,GWAS=NULL, GPS=NULL,Pred=NULL, REMLs=NULL,Timmer=Timmer,Memory=Memory,h2=NULL))
}
#QC
print("------------Examining data (QC)------------------------------------------")
if(is.null(Y)) stop ("GAPIT says: Phenotypes must exist.")
if(is.null(KI)&missing(GD) & kinship.algorithm!="SUPER") stop ("GAPIT says: Kinship is required. As genotype is not provided, kinship can not be created.")
#When GT and GD are missing, force to have fake ones (creating them from Y),GI is not required in this case
if(is.null(GD) & is.null(GT)) {
GT=as.matrix(Y[,1])
GD=matrix(1,nrow(Y),1)
GI=as.data.frame(matrix(0,1,3) )
colnames(GI)=c("SNP","Chromosome","Position")
}
if(is.null(GT)) {
GT=as.character(Y[,1])
}
#print("@@@@@@@@")
#print(GD)
#merge CV with PC: Put CV infront of PC
if(PCA.total>0&!is.null(CV))CV=GAPIT.CVMergePC(CV,PC)
if(PCA.total>0&is.null(CV))CV=PC
#for GS merge CV with GD name
if (is.null(CV))
{my_allCV=CV
}else{
taxa_GD=rownames(GD)
my_allCV=CV[order(CV[,1]),]
my_allCV=my_allCV[my_allCV[,1]%in%taxa_GD,]
#print(dim(my_allCV))
}
#Handler of CV.Inheritance
if(is.null(CV) & !is.null(CV.Inheritance)){
stop ("GAPIT says: CV.Inheritance is more than avaiable.")
}
if(!is.null(CV)& !is.null(CV.Inheritance)){
if(CV.Inheritance>(ncol(CV)-1)) stop ("GAPIT says: CV.Inheritance is more than avaiable.")
}
#Create Z as identity matrix from Y if it is not provided
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & is.null(Z)){
taxa=as.character(Y[,1]) #this part will make GS without CV not present all prediction
Z=as.data.frame(diag(1,nrow(Y)))
#taxa=as.character(KI[,1])
#Z=as.data.frame(diag(1,nrow(KI)))
Z=rbind(taxa,Z)
taxa=c('Taxa',as.character(taxa))
Z=cbind(taxa,Z)
}
ZI=Z
#Add the part of non proportion in Z matrix
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & !is.null(Z))
{
if(nrow(Z)-1<nrow(Y)) Z=GAPIT.ZmatrixFormation(Z=Z,Y=Y)
}
#Create CV with all 1's if it is not provided
noCV=FALSE
if(is.null(CV)){
noCV=TRUE
CV=Y[,1:2]
CV[,2]=1
colnames(CV)=c("taxa","overall")
}
#Remove duplicat and integragation of data
print("QC is in process...")
CVI <- CV
# print(dim(Z))
if(QC)
{
qc <- GAPIT.QC(Y=Y,KI=KI, GT=GT,CV=CV,Z=Z,GK=GK)
GTindex=qc$GTindex
Y=qc$Y
KI=qc$KI
CV=qc$CV
Z=qc$Z
GK=qc$GK
if(noCV)CVI=qc$CV #this part will make GS without CV not present all prediction
my_taxa=as.character(KI[,1])
}
#print(GTindex)
#print(dim(KI))
#Output phenotype
colnames(Y)=c("Taxa",name.of.trait)
if(file.output)
{try(write.table(Y, paste("GAPIT.", name.of.trait,".phenotype.csv" ,sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE))
}
#TDP
if(kinship.algorithm=="None" )
{
if(min(CV[,2])==max(CV[,2])) CV=NULL
theTDP=GAPIT.TDP(Y=Y,CV=CV,SNP=as.data.frame(cbind(GT[GTindex],as.matrix(as.data.frame(GD[GTindex,])))),
QTN=QTN, Round=QTN.round,QTN.limit=QTN.limit, QTN.update=QTN.update, Method=QTN.method)
#print(dim(GM))
#print(length(theTDP$p))
theGWAS=cbind(GM,theTDP$p,NA,NA,NA)
return (list(Compression=NULL,kinship.optimum=NULL, kinship=NULL,PC=NULL,GWAS=theGWAS, GPS=NULL,Pred=NULL,REMLs=NULL,QTN=theTDP$QTN,Timmer=Timmer,Memory=Memory,h2= NULL))
}
rm(qc)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="QC")
Memory=GAPIT.Memory(Memory=Memory,Infor="QC")
#Get indicator of sangwich top and bottom
byPass.top=FALSE
byPass=FALSE
NOBLUP=FALSE
if(group.from<2&group.to<2) NOBLUP=TRUE
#if(!is.null(sangwich.bottom)) byPass=((sangwich.bottom=="FaST" | sangwich.bottom=="SUPER" | sangwich.bottom=="DC" )& is.null(GP) )
if(!is.null(sangwich.top)) byPass.top=((sangwich.top=="FaST" | sangwich.top=="SUPER" | sangwich.top=="DC" ) )
if(!is.null(sangwich.bottom)) byPass=((sangwich.bottom=="FaST" | sangwich.bottom=="SUPER" | sangwich.bottom=="DC" ) )
print("Try to group from and to were set to 1")
if(byPass){
print("group from and to were set to 1")
group.from=1
group.to=1
}
print("------------Examining data (QC) done-------------------------------------")
#Sagnwich top bun: To gep GP if it is not provided
if(!is.null(sangwich.top) & is.null(GP))
{
print("-------------------Sandwich top bun-----------------------------------")
#print(dim(GD))
#print(GD[1:5,1:5])
#Create GK if not provided
if(is.null(GK)){
# set.seed(1)
nY=floor(nrow(Y)*.9)
nG=ncol(GD)
if(nG>nY){snpsam=sample(1:nG,nY)}else{snpsam=1:nG}
GK=GD[GTindex,snpsam]
SNPVar=apply(as.matrix(GK),2,var)
GK=GK[,SNPVar>0]
GK=cbind(as.data.frame(GT[GTindex]),as.data.frame(GK)) #add taxa
}
#myGD=cbind(as.data.frame(GT),as.data.frame(GD))
file.output.temp=file.output
file.output=FALSE
#print(sangwich.top)
GP=GAPIT.Bread(Y=Y,CV=CV,Z=Z,KI=KI,GK=GK,GD=cbind(as.data.frame(GT),as.data.frame(GD)),GM=GI,method=sangwich.top,GTindex=GTindex,LD=LD,file.output=file.output)$GWAS
file.output=file.output.temp
GK=NULL
print("-------------------Sagnwich top bun: done-----------------------------")
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="SagnwichTop")
Memory=GAPIT.Memory(Memory=Memory,Infor="SagnwichTop")
#Sandwich burger and dressing
print("-------------------Sandwich burger and dressing------------------------")
#Handler of group boundry
if(group.from>group.to) stop("GAPIT says: group.to should be larger than group.from. Please correct them!")
if(is.null(CV) | (!is.null(CV) & group.to<(ncol(CV)+1))) {
#The minimum of group is 1 + number of columns in CV
group.from=1
group.to=1
warning("The upper bound of groups (group.to) is not sufficient. both boundries were set to a and GLM is performed!")
}
if(!is.null(CV)& group.from<1) {
group.from=1 #minimum of group is number of columns in CV
warning("The lower bound of groups should be 1 at least. It was set to 1!")
}
nk=1000000000
if(!is.null(KI)) nk=min(nk,nrow(KI))
if(!is.null(GK)) nk=min(nk,nrow(GK))
if(!is.null(KI))
{
if(group.to>nk) {
#group.to=min(nrow(KI),length(GTindex)) #maximum of group is number of rows in KI
group.to=nk #maximum of group is number of rows in KI
warning("The upper bound of groups is too high. It was set to the size of kinship!")
}
if(group.from>nk){
group.from=nk
warning("The lower bound of groups is too high. It was set to the size of kinship!")
}
}
if(!is.null(CV)){
if(group.to<=ncol(CV)+1) {
#The minimum of group is number of columns in CV
#group.from=ncol(CV)+2
#group.to=ncol(CV)+2
warning("The upper bound of groups (group.to) is not sufficient. both boundries were set to their minimum and GLM is performed!")
}
}
#bin.fold=ceiling(log2(bin.to/bin.from))
#bin.seq=0:bin.fold
#bin.level=bin.from*2^bin.seq
#Set upper bound for inclosure.to
if(inclosure.to>nrow(Y))inclosure.to=nrow(Y)-1
#set inclosure loop levels
bin.level=seq(bin.from,bin.to,by=bin.by)
inclosure=seq(inclosure.from,inclosure.to,by=inclosure.by)
#Optimization for group number, cluster algorithm and kinship type
GROUP=seq(group.to,group.from,by=-group.by)#The reverse order is to make sure to include full model
if(missing("kinship.cluster")) kinship.cluster=c("ward", "single", "complete", "average", "mcquitty", "median", "centroid")
if(missing("kinship.group")) kinship.group=c("Mean", "Max", "Min", "Median")
numSetting=length(GROUP)*length(kinship.cluster)*length(kinship.group)*length(bin.level)*length(inclosure)
#Reform Y, GD and CV into EMMA format
ys=as.matrix(Y[,2])
X0=as.matrix(CV[,-1])
CV.taxa=CVI[,1]
#print(length(ys))
#Initial
count=0
Compression=matrix(,numSetting,6)
colnames(Compression)=c("Type","Cluster","Group","REML","VA","VE")
#add indicator of overall mean
if(min(X0[,1])!=max(X0[,1])) X0 <- cbind(1, X0) #do not add overall mean if X0 has it already at first column
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="DataProcessing")
Memory=GAPIT.Memory(Memory=Memory,Infor="DataProcessing")
print("-------------------------Iteration in process--------------------------")
print(paste("Total iterations: ",numSetting,sep=""))
#Loop to optimize cluster algorithm, group number and kinship type
for (bin in bin.level){
for (inc in inclosure){
#Grill: update KI if GK or GP is provided
if(!byPass & (!is.null(GK) | !is.null(GP)))
{
print("Grilling KI...")
myGenotype<-GAPIT.Genotype(G=NULL,GD=cbind(as.data.frame(GT),as.data.frame(GD)),GM=GI,KI=NULL,kinship.algorithm=kinship.algorithm,PCA.total=0,SNP.fraction=SNP.fraction,SNP.test=SNP.test,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,
file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF=SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,kinship.cluster=kinship.cluster,NJtree.group=NJtree.group,NJtree.type=NJtree.type,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,
GP=GP,GK=GK,bin.size=bin,inclosure.size=inc,SNP.CV=SNP.CV,
Timmer = Timmer, Memory = Memory,GTindex=GTindex,sangwich.top=NULL,sangwich.bottom=sangwich.bottom,
file.output=file.output, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=myGenotype$Timmer
Memory=myGenotype$Memory
KI=myGenotype$KI
#update group set by new KI
nk=nrow(KI)
GROUP=GROUP[GROUP<=nk]
}
for (ca in kinship.cluster){
for (group in GROUP){
for (kt in kinship.group){
#Do not screen SNP unless existing genotype and one combination
if(numSetting==1 & hasGenotype){
optOnly=FALSE
}else{
optOnly=TRUE
}
if(!SNP.test) optOnly=TRUE
if(optOnly | Model.selection){
colInclude=1
optOnly = TRUE
}else{
colInclude=c(1:ncol(GD))
}
if(!optOnly) {print("Compressing and Genome screening..." )}
count=count+1
#Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 1")
#Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 1")
if(!byPass)
{
if(count==1)print("-------Mixed model with Kinship-----------------------------")
if(group<ncol(X0)+1) group=1 # the emma function (emma.delta.REML.dLL.w.Z) does not allow K has dim less then CV. turn to GLM (group=1)
cp <- GAPIT.Compress(KI=KI,kinship.cluster=ca,kinship.group=kt,GN=group,Timmer=Timmer,Memory=Memory)
Timmer=cp$Timmer
Memory=cp$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_cp")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2_cp")
#print("BK...")
bk <- GAPIT.Block(Z=Z,GA=cp$GA,KG=cp$KG)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_bk")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 bk")
#print("ZC...")
zc <- GAPIT.ZmatrixCompress(Z=Z,GAU =bk$GA)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_zc")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 zc")
#print("wraping...")
#Reform KW and Z into EMMA format
zrow=nrow(zc$Z)
zcol=ncol(zc$Z)-1
#Z1=matrix(as.numeric(as.matrix(zc$Z[,-1])),nrow=zrow,ncol=zcol)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Prio PreP3D")
Memory=GAPIT.Memory(Memory=Memory,Infor="Prio PreP3D")
#Evaluating maximum likelohood
#print("Calling EMMAxP3D...")
#print("It made it to here")
#print("The dimension of xs is:")
#print("The value of SNP.impute is")
#print(SNP.impute)
#write.table(zc$Z, "Z.csv", quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#print(dim(as.matrix(as.data.frame(GD[GTindex,colInclude]))))
#print("!!!!!!!!!!!!")
#print(length(ys))
#print(GTindex)
#print(dim(GD))
#print(dim(as.matrix(as.data.frame(GD[GTindex,colInclude]))))
#print(dim(GI))
p3d <- GAPIT.EMMAxP3D(ys=ys,xs=as.matrix(as.data.frame(GD[GTindex,colInclude])),K = as.matrix(bk$KW) ,Z=matrix(as.numeric(as.matrix(zc$Z[,-1])),nrow=zrow,ncol=zcol),X0=X0,CVI=CVI,CV.Inheritance=CV.Inheritance,GI=GI,SNP.P3D=SNP.P3D,Timmer=Timmer,Memory=Memory,fullGD=fullGD,
SNP.permutation=SNP.permutation, GP=GP,SNP.fraction=SNP.fraction,
file.path=file.path,file.from=file.from,file.to=file.to,file.total=file.total, file.fragment = file.fragment, byFile=byFile, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
GTindex=GTindex,genoFormat=genoFormat,optOnly=optOnly,SNP.effect=SNP.effect,SNP.impute=SNP.impute,name.of.trait=name.of.trait, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=p3d$Timmer
Memory=p3d$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Post PreP3D")
Memory=GAPIT.Memory(Memory=Memory,Infor="Post PreP3D")
#print("Cluster algorithm, kinship type, groups, VG, Ve and REML:")
print(paste(count, "of",numSetting,"--","Vg=",round(p3d$vgs,4), "VE=",round(p3d$ves,4),"-2LL=",round(p3d$REMLs,2), " Clustering=",ca," Group number=", group ," Group kinship=",kt,sep = " "))
#print(table(GTindex))
#Recoding the optimum KI
if(count==1){
KI.save=KI
LL.save=p3d$REMLs
}else{
if(p3d$REMLs<LL.save){
KI.save=KI
LL.save=p3d$REMLs
}
}
#print(paste("CA is ",ca))
#print(paste("group is ",group))
#print(paste("kt is ",kt))
#recording Compression profile on array
Compression[count,1]=kt
Compression[count,2]=ca
Compression[count,3]=group
Compression[count,4]=p3d$REMLs
Compression[count,5]=p3d$vgs
Compression[count,6]=p3d$ves
#print("result saved")
}else{# end of if(!byPass)
#Set QTNs
if(count==1)print("-------The burger is SNP-----------------------------------")
#bin.size=bin
#inclosure.size=inc
#@@@This section is not useful
if(!is.null(GP))
{
#print("Being specific...")
myGenotype<-GAPIT.Genotype(G=NULL,GD=NULL,GM=GI,KI=NULL,kinship.algorithm="SUPER",PCA.total=0,SNP.fraction=SNP.fraction,SNP.test=SNP.test,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,
file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF=SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,kinship.cluster=kinship.cluster,#NJtree.group=NJtree.group,NJtree.type=NJtree.type,
GP=GP,GK=NULL,bin.size=bin,inclosure.size=inc,SNP.CV=SNP.CV,GTindex=GTindex,sangwich.top=NULL,sangwich.bottom=sangwich.bottom,
Timmer = Timmer, Memory = Memory,file.output=file.output, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=myGenotype$Timmer
Memory=myGenotype$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype for burger")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype for burger")
print(paste("bin---",bin,"---inc---",inc,sep=""))
GK=GD[GTindex,myGenotype$SNP.QTN]
SUPER_GD=GD[,myGenotype$SNP.QTN]
SNPVar=apply(as.matrix(GK),2,var)
GK=GK[,SNPVar>0]
SUPER_GD=SUPER_GD[,SNPVar>0]
GK=cbind(as.data.frame(GT[GTindex]),as.data.frame(GK)) #add taxa
SUPER_GD=cbind(as.data.frame(GT),as.data.frame(SUPER_GD)) #add taxa
#GP=NULL
}# end of if(is.null(GK))
if(!is.null(GK) & numSetting>1)
{
print("-------Calculating likelihood-----------------------------------")
# myBurger=GAPIT.Burger(Y=Y,CV=CV,GK=GK)
myBurger=GAPIT.Burger(Y=Y,CV=NULL,GK=GK) #########modified by Jiabo Wang
myREML=myBurger$REMLs
myVG=myBurger$vg
myVE=myBurger$ve
}else{
myREML=NA
myVG=NA
myVE=NA
}
#Recoding the optimum GK
if(count==1){
GK.save=GK
LL.save=myREML
SUPER_optimum_GD=SUPER_GD ########### get SUPER GD
}else{
if(myREML<LL.save){
GK.save=GK
LL.save=myREML
SUPER_optimum_GD=SUPER_GD ########### get SUPER GD
}
}
#Put to storage
Compression[count,1]=1
Compression[count,2]=bin
Compression[count,3]=inc
Compression[count,4]=myREML
Compression[count,5]=myVG
Compression[count,6]=myVG
print(Compression[count,])
#print("---------------SUPER 2nd stage: calculating LL ------------------------")
} # end of if(byPass)
}#end of for (ca in kinship.cluster)
#Skip the rest group in case group 1 is finished
if(group==1) break #To skip the rest group interations
}#end of for (group in GROUP)
}#end of for (kt in kinship.group)
}#end of for (inc in inclosure)
}#end of for (bin in bin.level)
if(Model.selection == TRUE){
print("------------------------Model selection for optimal number of PCs and Covariates-------------------------------------------------")
#update KI with the best likelihood
KI=KI.save
if(numSetting>1){
Compression=Compression[order(as.numeric(Compression[,4]),decreasing = FALSE),] #sort on REML
kt=Compression[1,1]
ca=Compression[1,2]
group=Compression[1,3]
}
cp <- GAPIT.Compress(KI=KI,kinship.cluster=ca,kinship.group=kt,GN=group,Timmer=Timmer,Memory=Memory)
Timmer=cp$Timmer
Memory=cp$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_cp")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2_cp")
bk <- GAPIT.Block(Z=Z,GA=cp$GA,KG=cp$KG)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_bk")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 bk")
zc <- GAPIT.ZmatrixCompress(Z=Z,GAU =bk$GA)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_zc")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 zc")
z0=as.matrix(zc$Z[,-1])
Z1=matrix(as.numeric(z0),nrow=nrow(z0),ncol=ncol(z0))
BIC <- rep(NA,ncol(X0))
LogLike <- rep(NA, ncol(X0))
for(i in 1:ncol(X0)){#1 because the first column of X0 is the intercept
X0.test <- as.matrix(X0[,1:i])
#print("The dim of bk$KW is ")
#print(dim(bk$KW))
#print(dim(X0.test))
#print(dim(CVI))
p3d <- GAPIT.EMMAxP3D(ys=ys,xs=as.matrix(as.data.frame(GD[,1])),K = as.matrix(bk$KW) ,Z=Z1,X0=X0.test,CVI=CVI,CV.Inheritance=CV.Inheritance,GI=GI,SNP.P3D=SNP.P3D,Timmer=Timmer,Memory=Memory,fullGD=fullGD,
SNP.permutation=SNP.permutation, GP=GP,
file.path=file.path,file.from=file.from,file.to=file.to,file.total=file.total, file.fragment = file.fragment, byFile=byFile, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
GTindex=GTindex,genoFormat=genoFormat,optOnly=TRUE,SNP.effect=SNP.effect,SNP.impute=SNP.impute,name.of.trait=name.of.trait, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
k.num.param <- 2+i
#k is (i-1) because we have the following parameters in the likelihood function:
# intercept
# (i-1) covariates
# sigma_g
# delta
#print(paste("The value of round(p3d$REMLs,5) is ", round(p3d$REMLs,5), sep = ""))
#print(paste("The value of log(GTindex) is ", log(GTindex), sep = ""))
#print(paste("The value of 0.5*k.num.param*log(GTindex) is ", 0.5*k.num.param*log(nrow(Z1)), sep = ""))
LogLike[i] <- p3d$logLM
BIC[i] <- p3d$logLM -(0.5*k.num.param*log(nrow(Z1)))
#print("The value of k.num.param is: ")
#print(k.num.param)
#print(paste("The value of nrow(Z1) is ", nrow(Z1), sep = ""))
}
Optimum.from.BIC <- which(BIC == max(BIC))
print(paste("-----------------------The optimal number of PCs/covariates is ", (Optimum.from.BIC-1)," -------------------------", sep = ""))
BIC.Vector <- cbind(as.matrix(rep(0:(ncol(X0)-1))), as.matrix(BIC), as.matrix(LogLike))
#print(seq(0:ncol(X0)))
#print(BIC.Vector)
colnames(BIC.Vector) <- c("Number of PCs/Covariates", "BIC (larger is better) - Schwarz 1978", "log Likelihood Function Value")
write.table(BIC.Vector, paste("GAPIT.", name.of.trait, ".BIC.Model.Selection.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#print(BIC.Vector)
X0 <- X0[,1:(Optimum.from.BIC)]
if(Optimum.from.BIC == 1){
X0 <- as.matrix(X0)
}
print("The dimension of X0 after model selection is:")
print(dim(X0))
print("The head of X0 after model selection is")
print(head(X0))
} # where does it start: 522
print("---------------------Sandwich bottom bun-------------------------------")
print("Compression")
print(Compression)
#Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Compression")
#Memory=GAPIT.Memory(Memory=Memory,Infor="Copmression")
if(numSetting==1)
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GWAS")
Memory=GAPIT.Memory(Memory=Memory,Infor="GWAS")
}
#Perform GWAS with the optimum setting
#This section is omited if there is only one setting
if((numSetting>1)| (!is.null(sangwich.bottom)&!byPass) | Model.selection) {
print("Genomic screening..." )
optOnly=FALSE #set default to false and change it to TRUE in these situations:
if(!hasGenotype) optOnly=TRUE
if(!SNP.test) optOnly=TRUE
if(optOnly){
colInclude=1
}else{
colInclude=c(1:ncol(GD))
}
if(numSetting>1){
#Find the best ca,kt and group
print(paste(as.numeric(Compression[1,4]))) ###added by Jiabo Wang 2015.7.20
print(paste(min(as.numeric(Compression[,4]),rm.na=TRUE)))
adjust_value=as.numeric(Compression[1,4])-min(as.numeric(Compression[,4]),rm.na=TRUE)
nocompress_value=as.numeric(Compression[1,4])
REML_storage=as.numeric(Compression[,4])
adjust_mean=mean(as.numeric(Compression[,4]),rm.na=TRUE)
threshold=adjust_mean*0.1
if(adjust_value<3|nocompress_value<0) ###added by Jiabo Wang 2015.7.20
{
kt=Compression[1,1]
ca=Compression[1,2]
group=Compression[1,3]
print(paste("Optimum: ",Compression[1,2],Compression[1,1],Compression[1,3],Compression[1,5], Compression[1,6],Compression[1,4] ,sep = " "))
}else{
Compression=Compression[order(as.numeric(Compression[,4]),decreasing = FALSE),] #sort on REML
kt=Compression[1,1]
ca=Compression[1,2]
group=Compression[1,3]
print(paste("Optimum: ",Compression[1,2],Compression[1,1],Compression[1,3],Compression[1,5], Compression[1,6],Compression[1,4] ,sep = " "))
}
}#end if(numSetting>1)
print("-------------- Sandwich bottom ------------------------")
if(!byPass)
{
print("-------------- Sandwich bottom with raw burger------------------------")
if(Model.selection == FALSE){
#update KI with the best likelihood
if(is.null(sangwich.bottom)) KI=KI.save
cp <- GAPIT.Compress(KI=KI,kinship.cluster=ca,kinship.group=kt,GN=group,Timmer=Timmer,Memory=Memory)
Timmer=cp$Timmer
Memory=cp$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_cp")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2_cp")
bk <- GAPIT.Block(Z=Z,GA=cp$GA,KG=cp$KG)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_bk")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 bk")
zc <- GAPIT.ZmatrixCompress(Z=Z,GAU =bk$GA)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="PreP3D 2_zc")
Memory=GAPIT.Memory(Memory=Memory,Infor="PreP3D 2 zc")
#Reform KW and Z into EMMA format
z0=as.matrix(zc$Z[,-1])
Z1=matrix(as.numeric(z0),nrow=nrow(z0),ncol=ncol(z0))
}
print("--------------EMMAxP3D with the optimum setting-----------------------")
#print(dim(ys))
#print(dim(as.matrix(as.data.frame(GD[GTindex,colInclude]))))
p3d <- GAPIT.EMMAxP3D(ys=ys,xs=as.matrix(as.data.frame(GD[GTindex,colInclude])) ,K = as.matrix(bk$KW) ,Z=Z1,X0=as.matrix(X0),CVI=CVI, CV.Inheritance=CV.Inheritance,GI=GI,SNP.P3D=SNP.P3D,Timmer=Timmer,Memory=Memory,fullGD=fullGD,
SNP.permutation=SNP.permutation, GP=GP,
file.path=file.path,file.from=file.from,file.to=file.to,file.total=file.total, file.fragment = file.fragment, byFile=byFile, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
GTindex=GTindex,genoFormat=genoFormat,optOnly=optOnly,SNP.effect=SNP.effect,SNP.impute=SNP.impute,name.of.trait=name.of.trait, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GWAS")
Memory=GAPIT.Memory(Memory=Memory,Infor="GWAS")
print("--------------EMMAxP3D with the optimum setting done------------------")
}#end of if(!byPass)
}#end of if(numSetting>1 & hasGenotype & !SNP.test)
#print("Screening wiht the optimum setting done")
if(byPass)
{
print("---------------Sandwich bottom with grilled burger---------------------")
print("---------------Sandwich bottom: reload bins ---------------------------")
#SUPER: Final screening
GK=GK.save
myBread=GAPIT.Bread(Y=Y,CV=CV,Z=Z,GK=GK,GD=cbind(as.data.frame(GT),as.data.frame(GD)),GM=GI,method=sangwich.bottom,GTindex=GTindex,LD=LD,file.output=file.output)
print("SUPER saving results...")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GWAS")
Memory=GAPIT.Memory(Memory=Memory,Infor="GWAS")
} #end of if(byPass)
print("--------------------Final results presentations------------------------")
#Plotting optimum group kinship
if(!byPass)
{
if(length(bk$KW)>1 &length(bk$KW)<length(KI) & length(bk$KW)<1000 &GAPIT3.output){
pdf(paste("GAPIT.",name.of.trait,".Kin.Optimum.pdf",sep=""), width = 12, height = 12)
par(mar = c(25,25,25,25))
heatmap.2(as.matrix(bk$KW), cexRow =.2, cexCol = 0.2, col=rev(heat.colors(256)), scale="none", symkey=FALSE, trace="none")
dev.off()
}
}
#Merge GWAS resultss from files to update ps,maf and nobs in p3d
if(byFile&!fullGD)
{
print("Loading GWAS results from file...")
for (file in file.from:file.to)
{
#Initicalization
frag=1
numSNP=file.fragment
while(numSNP==file.fragment) { #this is problematic if the read end at the last line
#Initicalization GI to detect reading empty line
#theGI=NULL
#theP=NULL
#theMAF=NULL
#thenobs=NULL
#reload results from files
print(paste("Current file ",file,"Fragment: ",frag))
theGI <- try(read.table(paste("GAPIT.TMP.GI.",name.of.trait,file,".",frag,".txt",sep=""), head = TRUE) ,silent=TRUE)
theP <- try(read.table(paste("GAPIT.TMP.ps.",name.of.trait,file,".",frag,".txt",sep=""), head = FALSE) ,silent=TRUE)
theMAF <- try(read.table(paste("GAPIT.TMP.maf.",name.of.trait,file,".",frag,".txt",sep=""), head = FALSE),silent=TRUE)
thenobs <- try(read.table(paste("GAPIT.TMP.nobs.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
thersquare_base <- try(read.table(paste("GAPIT.TMP.rsquare.base.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
thersquare <- try(read.table(paste("GAPIT.TMP.rsquare.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
thedf <- try(read.table(paste("GAPIT.TMP.df.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
thetvalue <- try(read.table(paste("GAPIT.TMP.tvalue.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
thestderr <- try(read.table(paste("GAPIT.TMP.stderr.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
theeffect.est <- try(read.table(paste("GAPIT.TMP.effect.est.",name.of.trait,file,".",frag,".txt",sep=""),head= FALSE),silent=TRUE)
if(inherits(theGI, "try-error")) {
#if(nrow(theGI)<1){
numSNP=0
#print("This fragment is empty.")
}else{
#print("Records loaded for this fragment.")
numSNP=nrow(theGI)
colnames(theP)="P"
colnames(theMAF )="MAF"
colnames(thenobs )="nobs"
colnames(thersquare_base) = "Base.Model.R.square"
colnames(thersquare) = "Model.R.square"
colnames(thedf) = "Model.DF"
colnames(thetvalue) = "Model.tvalue"
colnames(thestderr) = "Model.stderr"
colnames(theeffect.est) = "Effect.Est"
colnames(theGI) = colnames(GI)
#Merge results
if(file==file.from & frag==1){
GI=theGI
#print(dim(GI))
allP=theP
#print(head(theP))
allMAF=theMAF
allnobs=thenobs
allrsquare_base=thersquare_base
allrsquare=thersquare
alldf=thedf
alltvalue=thetvalue
allstderr=thestderr
alleffect.est=theeffect.est
}else{
allP=as.data.frame(rbind(as.matrix(allP),as.matrix(theP)) )
allMAF=as.data.frame(rbind(as.matrix(allMAF),as.matrix(theMAF)) )
allnobs=as.data.frame(rbind(as.matrix(allnobs),as.matrix(thenobs)))
allrsquare_base=as.data.frame(rbind(as.matrix(allrsquare_base),as.matrix(thersquare_base)))
allrsquare=as.data.frame(rbind(as.matrix(allrsquare),as.matrix(thersquare)))
alldf=as.data.frame(rbind(as.matrix(alldf),as.matrix(thedf)))
alltvalue=as.data.frame(rbind(as.matrix(alltvalue),as.matrix(thetvalue)))
allstderr=as.data.frame(rbind(as.matrix(allstderr),as.matrix(thestderr)))
alleffect.est=as.data.frame(rbind(as.matrix(alleffect.est),as.matrix(theeffect.est)))
#print("!!!!!!!!!!!!!!!")
#print(dim(GI))
#print(dim(theGI))
GI=as.data.frame(rbind(as.matrix(GI),as.matrix(theGI)))
}
}#end of if(inherits(theGI, "try-error")) (else section)
#setup for next fragment
frag=frag+1 #Progress to next fragment
}#end of loop on fragment: while(numSNP==file.fragment)
}#end of loop on file
#update p3d with components from files
p3d$ps=allP
p3d$maf=allMAF
p3d$nobs=allnobs
p3d$rsquare_base=allrsquare_base
p3d$rsquare=allrsquare
p3d$df=alldf
p3d$tvalue=alltvalue
p3d$stderr=allstderr
p3d$effect.est=alleffect.est
#Delete all the GAPIT.TMP files
theFile=paste("GAPIT.TMP.",name.of.trait,".*")
system('cmd /c del "GAPIT.TMP*.*"')
system('cmd /c del "GAPIT.TMP*.*"')
print("GWAS results loaded from all files succesfully!")
} #end of if(byFile)
#--------------------------------------------------------------------------------------------------------------------#
#Final report
print("Generating summary" )
GWAS=NULL
GPS=NULL
rm(zc)
gc()
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Final")
Memory=GAPIT.Memory(Memory=Memory,Infor="Final")
#genomic prediction
print("Genomic Breeding Values (GBV) ..." )
#print(p3d$BLUP)
gs=NULL
if(!byPass)
{
if(length(bk$KW)>ncol(X0)) {
gs <- GAPIT.GS(KW=bk$KW,KO=bk$KO,KWO=bk$KWO,GAU=bk$GAU,UW=cbind(p3d$BLUP,p3d$PEV))
}
print("Writing GBV and Acc..." )
GPS=NULL
if(length(bk$KW)>ncol(X0)) GPS=gs$BLUP
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GPS")
Memory=GAPIT.Memory(Memory=Memory,Infor="GPS")
#Make heatmap for distribution of BLUP and PEV
print("GBV and accuracy distribution..." )
if(length(bk$KW)>ncol(X0) &file.output) {
GAPIT.GS.Visualization(gsBLUP = gs$BLUP, BINS=BINS,name.of.trait = name.of.trait)
}
#Make a plot Summarzing the Compression Results, if more than one "compression level" has been assessed
print("Compression portfolios..." )
#print(Compression)
if(file.output) GAPIT.Compression.Visualization(Compression = Compression, name.of.trait = name.of.trait)
print("Compression Visualization done")
if(length(Compression)<1){
h2.opt= NULL
}else{
if(length(Compression)<=6) Compression=t(as.matrix(Compression[which(Compression[,4]!="NULL" | Compression[,4]!="NaN"),]))
if(length(Compression)==6) Compression=matrix(Compression,1,6)
if(length(Compression)>6) Compression=Compression[which(Compression[,4]!="NULL" | Compression[,4]!="NaN"),]
Compression.best=Compression[1,]
variance=as.numeric(Compression.best[5:6])
varp=variance/sum(variance)
h2.opt= varp[1]
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Compression.Visualization")
Memory=GAPIT.Memory(Memory=Memory,Infor="Compression.Visualization")
# print("$$$$$")
# print(str(p3d))
ps=p3d$ps
nobs=p3d$nobs
maf=p3d$maf
rsquare_base=p3d$rsquare_base
rsquare=p3d$rsquare
df=p3d$df
tvalue=p3d$tvalue
stderr=p3d$stderr
effect.est=p3d$effect.est
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Extract p3d results")
Memory=GAPIT.Memory(Memory=Memory,Infor="Extract p3d results")
print("p3d objects transfered")
#where does it start: 936
}else{ #byPass
#print("The head of myBread$GWAS is")
#print(head(myBread$GWAS))
GPS=myBread$BLUP
ps=myBread$GWAS[,4]
nobs=myBread$GWAS[,6]
#print(dim(GI))
#print(head())
Bread_index=match(as.character(myBread$GWAS[,1]),as.character(GI[,1]))
#print(GD[1:5,1:5])
Bread_X=GD[,Bread_index]
#print(dim(Bread_X))
maf=apply(Bread_X,2,function(one) abs(1-sum(one)/(2*nrow(Bread_X))))
maf[maf>0.5]=1-maf[maf>0.5]
rsquare_base=rep(NA,length(ps))
rsquare=rep(NA,length(ps))
df=rep(NA,length(nobs))
tvalue=rep(NA,length(nobs))
stderr=rep(NA,length(nobs))
effect.est=rep(NA,length(nobs))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Extract bread results")
Memory=GAPIT.Memory(Memory=Memory,Infor="Extract bread results")
}
print("Merge BLUP and BLUE")
#print(head(ps))
#Merge BLUP and BLUE
Pred=NULL
if((!byPass)&(!Model.selection)){
print("GAPIT before BLUP and BLUE")
#print(dim(p3d$BLUE))
BLUE=data.frame(cbind(data.frame(CV.taxa),data.frame(p3d$BLUE)))
colnames(BLUE)=c("Taxa","BLUE")
#Initial BLUP as BLUe and add additional columns
gs.blup=cbind(BLUE,NA,NA,0,NA)
if(!is.null(gs))gs.blup=gs$BLUP
BB= merge(gs.blup, BLUE, by.x = "Taxa", by.y = "Taxa")
if (is.null(my_allCV)){my_allX=matrix(1,length(my_taxa),1)
}else{
# my_allX=as.matrix(my_allCV[,-1])
my_allX=cbind(1,as.matrix(my_allCV[,-1]))
}
#print(dim(my_allX))
#print(head(my_allX))
#print(dim(BB))
#print(CV.Inheritance)
if(is.null(CV.Inheritance))
{
Prediction=BB[,5]+BB[,7]
Pred_Heritable=Prediction
}
if(!is.null(CV.Inheritance))
{
#inher_CV=my_allX[,1:(1+CV.Inheritance)]
#beta.Inheritance=p3d$effect.cv[1:(1+CV.Inheritance)]
#print(beta.Inheritance)
#if(length(beta)==1)CV=X
all_BLUE=try(my_allX%*%p3d$effect.cv,silent=T)
if(inherits(BLUE, "try-error")) all_BLUE = NA
Pred_Heritable=BB[,5]+BB[,7]
Prediction=BB[,5]+all_BLUE
}
#print("@@@@@@@@@@")
#print(dim(CVI))
#print(BB)
#CV.Inheritance
#Pred_Heritable=p3d$effect.cv[CV.Inheritance]%*%CVI[CV.Inheritance]+BB[,7]
Pred=data.frame(cbind(BB,data.frame(Prediction)),data.frame(Pred_Heritable))
if(noCV)
{
if(NOBLUP)
{Pred=NA
}else{
BLUE=Pred$BLUE[1]
prediction=as.matrix(GPS$BLUP)+(BLUE)
Pred=cbind(GPS,BLUE,prediction)
colnames(Pred)=c("Taxa","Group","RefInf","ID","BLUP","PEV","BLUE","Prediction")
}#end NOBLUP
}#end noCV
print("GAPIT after BLUP and BLUE")
}
#Export BLUP and PEV
if(!byPass &GAPIT3.output)
{
print("Exporting BLUP and Pred")
#try(write.table(gs$BLUP, paste("GAPIT.", name.of.trait,".BLUP.csv" ,sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE))
try(write.table(Pred, paste("GAPIT.", name.of.trait,".PRED.csv" ,sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE))
}
if(byPass)
{
theK.back=NULL
}else{
theK.back=cp$KG
}
if(byPass)Compression[1,4]=0 #create a fake value to aloow output of SUPER
#Export GWAS results
PWI.Filtered=NULL
if(hasGenotype &SNP.test &!is.na(Compression[1,4])) #require not NA REML
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Extract GWAS start")
Memory=GAPIT.Memory(Memory=Memory,Infor="Extract GWAS start")
#print("Filtering SNPs with MAF..." )
#index=maf>=SNP.MAF
PWI.Filtered=cbind(GI,ps,maf,nobs,rsquare_base,rsquare,effect.est)#[index,]
#print(dim(PWI.Filtered))
colnames(PWI.Filtered)=c("SNP","Chromosome","Position ","P.value", "maf", "nobs", "Rsquare.of.Model.without.SNP","Rsquare.of.Model.with.SNP","effect")
if(!byPass){
if(Create.indicator){
#Add a counter column for GI
GI.counter <- cbind(GI, seq(1:nrow(GI)))
#Turn GI and effect.est into data frames
GI.counter.data.frame <- data.frame(GI.counter)
colnames(GI.counter.data.frame) <- c("X1", "X2", "X3", "X4")
effect.est.data.frame <- data.frame(effect.est)
colnames(effect.est.data.frame) <- c("X1", "X2", "X3")
print(head(GI.counter.data.frame))
print(head(effect.est.data.frame))
#Do a merge statement
GWAS.2 <- merge(GI.counter.data.frame, effect.est.data.frame, by.x = "X4", by.y = "X1")
#Remove the counter column
GWAS.2 <- GWAS.2[,-1]
#Add column names
colnames(GWAS.2) <- c("SNP","Chromosome","Position ", "Genotype", "Allelic Effect Estimate")
}
if(!Create.indicator){
GWAS.2 <- PWI.Filtered[,c(1:3,9)]
colnames(GWAS.2) <- c("SNP","Chromosome","Position ", "Allelic Effect Estimate")
}
}
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="MAF filtered")
Memory=GAPIT.Memory(Memory=Memory,Infor="MAF filtered")
#print("SNPs filtered with MAF")
if(!is.null(PWI.Filtered))
{
#Run the BH multiple correction procedure of the results
#Create PWIP, which is a table of SNP Names, Chromosome, bp Position, Raw P-values, FDR Adjusted P-values
#print("Calculating FDR..." )
PWIP <- GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure(PWI = PWI.Filtered, FDR.Rate = FDR.Rate, FDR.Procedure = "BH")
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Multiple Correction")
Memory=GAPIT.Memory(Memory=Memory,Infor="Multiple Correction")
#QQ plots
#print("QQ plot..." )
if(file.output) GAPIT.QQ(P.values = PWIP$PWIP[,4], name.of.trait = name.of.trait,DPP=DPP)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="QQ plot")
Memory=GAPIT.Memory(Memory=Memory,Infor="QQ plot")
#Manhattan Plots
#print("Manhattan plot (Genomewise)..." )
# if(file.output) GAPIT.Manhattan(GI.MP = PWIP$PWIP[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff)
# if(file.output) GAPIT.Manhattan(GI.MP = PWIP$PWIP[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff,seqQTN=QTN.position) #QTN does not work with sorted P
if(file.output) GAPIT.Manhattan(GI.MP = PWI.Filtered[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff,seqQTN=QTN.position,plot.style=plot.style,plot.bin=plot.bin,chor_taxa=chor_taxa)
#print("Manhattan plot (Chromosomewise)..." )
#if(file.output) GAPIT.Manhattan(GI.MP = PWIP$PWIP[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Chromosomewise",cutOff=cutOff)
if(file.output&SNP.fraction==1) GAPIT.Manhattan(GI.MP = PWI.Filtered[,2:4],GD=GD,CG=CG, name.of.trait = name.of.trait, DPP=DPP, plot.type = "Chromosomewise",cutOff=cutOff,plot.bin=plot.bin,chor_taxa=chor_taxa)
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Manhattan plot")
Memory=GAPIT.Memory(Memory=Memory,Infor="Manhattan plot")
#Association Table
#print("Association table..." )
#print(dim(PWIP$PWIP))
#GAPIT.Table(final.table = PWIP$PWIP, name.of.trait = name.of.trait,SNP.FDR=SNP.FDR)
#print(head(PWIP$PWIP))
GWAS=PWIP$PWIP[PWIP$PWIP[,9]<=SNP.FDR,]
#print("Joining tvalue and stderr" )
DTS=cbind(GI,df,tvalue,stderr,effect.est)
colnames(DTS)=c("SNP","Chromosome","Position","DF","t Value","std Error","effect")
#print("Creating ROC table and plot" )
if(file.output) myROC=GAPIT.ROC(t=tvalue,se=stderr,Vp=var(ys),trait=name.of.trait)
#print("ROC table and plot created" )
#MAF plots
#print("MAF plot..." )
if(file.output) myMAF1=GAPIT.MAF(MAF=GWAS[,5],P=GWAS[,4],E=NULL,trait=name.of.trait)
#print(dim(GWAS))
if(file.output){
write.table(GWAS, paste("GAPIT.", name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
write.table(DTS, paste("GAPIT.", name.of.trait, ".Df.tValue.StdErr.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
if(!byPass) write.table(GWAS.2, paste("GAPIT.", name.of.trait, ".Allelic_Effect_Estimates.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}
} #end of if(!is.null(PWI.Filtered))
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Extract GWAS end")
Memory=GAPIT.Memory(Memory=Memory,Infor="Extract GWAS end")
} #end of if(hasGenotype )
#Log
if(GAPIT3.output) log=GAPIT.Log(Y=Y,KI=KI,Z=Z,CV=CV,SNP.P3D=SNP.P3D,
group.from = group.from ,group.to =group.to ,group.by = group.by ,kinship.cluster = kinship.cluster, kinship.group= kinship.group,
ngrid = ngrid , llin = llin , ulim = ulim , esp = esp ,name.of.trait = name.of.trait)
#Memory usage
#GAPIT.Memory.Object(name.of.trait=name.of.trait)
#Timming
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Report")
Memory=GAPIT.Memory(Memory=Memory,Infor="Report")
if(file.output){
file=paste("GAPIT.", name.of.trait,".Timming.csv" ,sep = "")
write.table(Timmer, file, quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
file=paste("GAPIT.", name.of.trait,".Memory.Stage.csv" ,sep = "")
write.table(Memory, file, quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}
print(paste(name.of.trait, "has been analyzed successfully!") )
print(paste("The results are saved in the directory of ", getwd()) )
#print("==========================================================================================")
TV<-list()
TV$ps=ps
TV$nobs=nobs
TV$maf=maf
TV$rsquare_base=rsquare_base
TV$rsquare=rsquare
TV$df=df
TV$tvalue=tvalue
TV$stderr=stderr
TV$effect.est=effect.est
#print("!!!!!!!!!!!!!")
#print(head(effect.est))
#print(head(DTS[,7]))
#print(ys)
if(byPass | Model.selection) Pred <- NA
print("before ending GAPIT.Main")
#print(dim(Compression))
return (list(Timmer=Timmer,Compression=Compression,kinship.optimum=theK.back, kinship=KI,PC=PC,GWAS=PWI.Filtered, GPS=GPS,Pred=Pred,REMLs=Compression[count,4],Timmer=Timmer,Memory=Memory,SUPER_GD=SUPER_GD,P=ps,effect.snp=DTS[,7],effect.cv=p3d$effect.cv,h2= h2.opt,TV=TV))
} #end if non-SUPER.GS situation, this is a long if statement, structure needs improvement
}#The function GAPIT.Main ends here
#=============================================================================================
`GAPIT.Manhattan` <-
function(GI.MP = NULL,GD=NULL,name.of.trait = "Trait",plot.type = "Genomewise",
DPP=50000,cutOff=0.01,band=5,seqQTN=NULL,plot.style="Oceanic",CG=NULL,plot.bin=10^9,chor_taxa=NULL){
#Object: Make a Manhattan Plot
#Options for plot.type = "Separate_Graph_for_Each_Chromosome" and "Same_Graph_for_Each_Chromosome"
#Output: A pdf of the Manhattan Plot
#Authors: Alex Lipka, Zhiwu Zhang, Meng Li and Jiabo Wang
# Last update: Oct 10, 2016
#Add r2 between candidata SNP and other markers in on choromosome
##############################################################################################
#print("Manhattan ploting...")
#print(cutOff)
#do nothing if null input
if(is.null(GI.MP)) return
#if(is.null(GD)) return
#print("Dimension of GI.MP")
#print(dim(GI.MP))
#print(head(GI.MP))
#print(tail(GI.MP))
#print(CG)
#seqQTN=c(300,1000,2500)
#Handler of lable paosition only indicated by negatie position
position.only=F
if(!is.null(seqQTN)){
if(seqQTN[1]<0){
seqQTN=-seqQTN
position.only=T
}
}
#if(is.null(GD)) print ("GD is not same dim as GM")
borrowSlot=4
GI.MP[,borrowSlot]=0
GI.MP[,5]=1:(nrow(GI.MP))
GI.MP=matrix(as.numeric(as.matrix(GI.MP) ) ,nrow(GI.MP),ncol(GI.MP))
GI.MP=GI.MP[order(GI.MP[,2]),]
GI.MP=GI.MP[order(GI.MP[,1]),]
# print("@@@@@")
# print(head(GI.MP))
#Inicial as 0
if(!is.null(seqQTN))GI.MP[seqQTN,borrowSlot]=1
if(!is.null(GD))
{ if(ncol(GD)!=nrow(GI.MP))print("GD does not mach GM in Manhattan !!!")
}
#print(ncol(GD))
#print(nrow(GI.MP))
#print(GI.MP)
#print("!!")
#GI.MP[,5]=1:(nrow(GI.MP))
#print(head(GI.MP,20))
#Remove all SNPs that do not have a choromosome, bp position and p value(NA)
GI.MP <- GI.MP[!is.na(GI.MP[,1]),]
GI.MP <- GI.MP[!is.na(GI.MP[,2]),]
if(!is.null(GD)) GD=GD[,!is.na(GI.MP[,3])]
GI.MP <- GI.MP[!is.na(GI.MP[,3]),]
#Retain SNPs that have P values between 0 and 1 (not na etc)
if(!is.null(GD)) GD=GD[,GI.MP[,3]>0]
GI.MP <- GI.MP[GI.MP[,3]>0,]
if(!is.null(GD)) GD=GD[,GI.MP[,3]<=1]
GI.MP <- GI.MP[GI.MP[,3]<=1,]
#Remove chr 0 and 99
GI.MP <- GI.MP[GI.MP[,1]!=0,]
#GI.MP <- GI.MP[GI.MP[,1]!=99,]
#print(dim(GI.MP))
#print("Dimension of GI.MP after QC")
#print(dim(GI.MP))
#print(head(GI.MP))
numMarker=nrow(GI.MP)
#print(numMarker)
bonferroniCutOff=-log10(cutOff/numMarker)
#Replace P the -log10 of the P-values
if(!is.null(GD))
{ if(ncol(GD)!=nrow(GI.MP))
{print("GD does not match GM in Manhattan !!!")
return
}}
#print(ncol(GD))
#print(nrow(GI.MP))
GI.MP[,3] <- -log10(GI.MP[,3])
index_GI=GI.MP[,3]>0
GI.MP <- GI.MP[index_GI,]
if(!is.null(GD)) GD=GD[,index_GI]
GI.MP[,5]=1:(nrow(GI.MP))
y.lim <- ceiling(max(GI.MP[,3]))
chm.to.analyze <- unique(GI.MP[,1])
#print(dim(GI.MP))
#print(dim(GD))
#print("name of chromosomes:")
#print(chm.to.analyze)
chm.to.analyze=chm.to.analyze[order(chm.to.analyze)]
numCHR= length(chm.to.analyze)
#GI.MP[,5]=1:(nrow(GI.MP))
bin.mp=GI.MP[,1:3]
bin.mp[,3]=0 # for r2
bin.mp[,1]=as.numeric(as.vector(GI.MP[,2]))+as.numeric(as.vector(GI.MP[,1]))*(10^(max(GI.MP[,1])+1))
#as.numeric(as.vector(GP[,3]))+as.numeric(as.vector(GP[,2]))*MaxBP
#print(head(bin.mp))
bin.mp[,2]=floor(bin.mp[,1]/plot.bin)
if(!is.null(GD)) X=GD
#print(head(bin.mp))
#Chromosomewise plot
if(plot.type == "Chromosomewise"&!is.null(GD))
{
#print("Manhattan ploting Chromosomewise")
GI.MP=cbind(GI.MP,bin.mp)
pdf(paste("GAPIT.", name.of.trait,".Manhattan.Plot.Chromosomewise.pdf" ,sep = ""), width = 10)
#par(mar = c(5,5,4,3), lab = c(8,5,7))
layout(matrix(c(1,1,2,1,1,1,1,1,1),3,3,byrow=TRUE), c(2,1), c(1,1), TRUE)
for(i in 1:numCHR)
{
#Extract SBP on this chromosome
subset=GI.MP[GI.MP[,1]==chm.to.analyze[i],,drop=FALSE]
# print(head(subset))
if(nrow(subset)==0)next #thanks to lvclark to fix it
subset[,1]=1:(nrow(subset))
#sub.bin.mp=bin.mp[GI.MP[,1]==chm.to.analyze[i],]
#subset=cbind(subset,sub.bin.mp)
sig.mp=subset[subset[,3]>bonferroniCutOff,,drop=FALSE]
sig.index=subset[,3]>bonferroniCutOff ### index of significont SNP
num.row=nrow(sig.mp)
if(!is.null(dim(sig.mp)))sig.mp=sig.mp[!duplicated(sig.mp[,7]),]
num.row=nrow(sig.mp)
if(is.null(dim(sig.mp))) num.row=1
bin.set=NULL
r2_color=matrix(0,nrow(subset),2)
#r2_color
print(paste("select ",num.row," candidate significont markers in ",i," chromosome ",sep="") )
#print(sig.mp)
if(length(unique(sig.index))==2)
{
for(j in 1:num.row)
{ sig.mp=matrix(sig.mp,num.row,8)
#print(sig.mp[j,7])
#print(unique(subset[,7]))
bin.store=subset[which(subset[,7]==sig.mp[j,7]),]
if(is.null(dim(bin.store)))
{subset[which(subset[,7]==sig.mp[j,7]),8]=1
next
}
bin.index=unique(bin.store[,5])
subGD=X[,bin.store[,5]]
#print(dim(bin.store))
if(is.null(CG))candidata=bin.store[bin.store[,3]==max(bin.store[,3]),5]
if(length(candidata)!=1)candidata=candidata[1]
for (k in 1:ncol(subGD))
{
r2=cor(X[,candidata],subGD[,k])^2
#print(r2)
bin.store[k,8]=r2
}
#print(bin.store)
#r2_storage[is.na(r2_storage)]=0
#print(bin.store)
subset[bin.store[,1],8]=bin.store[,8]
#print()
}###end for each sig.mp
#sub.bin.mp=bin.mp[subset[,3]>bonferroniCutOff,]
#print(head(bin.set))
}###end if empty of sig.mp
#print("@@@@@@@@@@@@@@@@")
rm(sig.mp,num.row)
#print(head(subset))
#print(head(subset))
#print(dim(X))
y.lim <- ceiling(max(subset[,3]))+1 #set upper for each chr
if(length(subset)>3){
x <- as.numeric(subset[,2])/10^(6)
y <- as.numeric(subset[,3])
}else{
x <- as.numeric(subset[2])/10^(6)
y <- as.numeric(subset[3])
}
##print(paste("befor prune: chr: ",i, "length: ",length(x),"max p",max(y), "min p",min(y), "max x",max(x), "Min x",min(x)))
n_col=10
r2_color[,2]=subset[,8]
do_color=colorRampPalette(c("orangeRed", "blue"))(n_col)
#Prune most non important SNPs off the plots
order=order(y,decreasing = TRUE)
y=y[order]
x=x[order]
r2_color=r2_color[order,,drop=FALSE]
index=GAPIT.Pruning(y,DPP=round(DPP/numCHR))
x=x[index]
y=y[index]
r2_color=r2_color[index,,drop=FALSE]
r2_color[which(r2_color[,2]<=0.2),2]=do_color[n_col]
r2_color[which(r2_color[,2]<=0.4&r2_color[,2]>0.2),2]=do_color[n_col*0.8]
r2_color[which(r2_color[,2]<=0.6&r2_color[,2]>0.4),2]=do_color[n_col*0.6]
r2_color[which(r2_color[,2]<=0.8&r2_color[,2]>0.6),2]=do_color[n_col*0.4]
r2_color[which(r2_color[,2]<=1&r2_color[,2]>0.8),2]=do_color[n_col/n_col]
#print(unique(r2_color[,2]))
##print(paste("after prune: chr: ",i, "length: ",length(x),"max p",max(y), "min p",min(y), "max x",max(x), "Min x",min(x)))
par(mar=c(0,0,0,0))
par(mar=c(5,5,2,1),cex=0.8)
plot(y~x,type="p", ylim=c(0,y.lim), xlim = c(min(x), max(x)),
col = r2_color[,2], xlab = expression(Base~Pairs~(x10^-6)),
ylab = "-Log Base 10 p-value", main = paste("Chromosome",chm.to.analyze[i],sep=" "),
cex.lab=1.6,pch=21,bg=r2_color[,2])
abline(h=bonferroniCutOff,col="forestgreen")
##print("manhattan plot (chr) finished")
#layout.show(nf)
#provcol <-c("darkblue","cyan","green3","brown1","brown1")
#provcol <-heat.colors(50)
#par(mar=c(0,0,0,0))
par(mar=c(15,5,6,5),cex=0.5)
barplot(matrix(rep(1,times=n_col),n_col,1),beside=T,col=do_color,border=do_color,axes=FALSE,)
#legend(x=10,y=2,legend=expression(R^"2"),,lty=0,cex=1.3,bty="n",bg=par("bg"))
axis(3,seq(11,1,by=-2),seq(0,1,by=0.2))
}# end plot.type == "Chromosomewise"&!is.null(GD)
dev.off()
print("manhattan plot on chromosome finished")
} #Chromosomewise plot
#Genomewise plot
if(plot.type == "Genomewise")
{
#print("Manhattan ploting Genomewise")
#Set corlos for chromosomes
#nchr=max(chm.to.analyze)
nchr=length(chm.to.analyze)
#Set color schem
ncycle=ceiling(nchr/band)
ncolor=band*ncycle
#palette(rainbow(ncolor+1))
cycle1=seq(1,nchr,by= ncycle)
thecolor=cycle1
for(i in 2:ncycle){thecolor=c(thecolor,cycle1+(i-1))}
col.Rainbow=rainbow(ncolor+1)[thecolor]
col.FarmCPU=rep(c("#CC6600","deepskyblue","orange","forestgreen","indianred3"),ceiling(numCHR/5))
col.Rushville=rep(c("orangered","navyblue"),ceiling(numCHR/2))
col.Congress=rep(c("deepskyblue3","firebrick"),ceiling(numCHR/2))
col.Ocean=rep(c("steelblue4","cyan3"),ceiling(numCHR/2))
col.PLINK=rep(c("gray10","gray70"),ceiling(numCHR/2))
col.Beach=rep(c("turquoise4","indianred3","darkolivegreen3","red","aquamarine3","darkgoldenrod"),ceiling(numCHR/5))
#col.Oceanic=rep(c( '#EC5f67', '#F99157', '#FAC863', '#99C794', '#5FB3B3', '#6699CC', '#C594C5', '#AB7967'),ceiling(numCHR/8))
#col.Oceanic=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5', '#AB7967'),ceiling(numCHR/6))
col.Oceanic=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(numCHR/5))
col.cougars=rep(c( '#990000', 'dimgray'),ceiling(numCHR/2))
if(plot.style=="Rainbow")plot.color= col.Rainbow
if(plot.style =="FarmCPU")plot.color= col.Rainbow
if(plot.style =="Rushville")plot.color= col.Rushville
if(plot.style =="Congress")plot.color= col.Congress
if(plot.style =="Ocean")plot.color= col.Ocean
if(plot.style =="PLINK")plot.color= col.PLINK
if(plot.style =="Beach")plot.color= col.Beach
if(plot.style =="Oceanic")plot.color= col.Oceanic
if(plot.style =="cougars")plot.color= col.cougars
#FarmCPU uses filled dots
mypch=1
if(plot.style =="FarmCPU")mypch=20
GI.MP <- GI.MP[order(GI.MP[,2]),]
GI.MP <- GI.MP[order(GI.MP[,1]),]
ticks=NULL
lastbase=0
#print("Manhattan data sorted")
#print(chm.to.analyze)
#change base position to accumulatives (ticks)
for (i in chm.to.analyze)
{
index=(GI.MP[,1]==i)
ticks <- c(ticks, lastbase+mean(GI.MP[index,2]))
GI.MP[index,2]=GI.MP[index,2]+lastbase
lastbase=max(GI.MP[index,2])
}
#print("Manhattan chr processed")
#print(length(index))
#print(length(ticks))
#print((ticks))
#print((lastbase))
x0 <- as.numeric(GI.MP[,2])
y0 <- as.numeric(GI.MP[,3])
z0 <- as.numeric(GI.MP[,1])
position=order(y0,decreasing = TRUE)
index0=GAPIT.Pruning(y0[position],DPP=DPP)
index=position[index0]
x=x0[index]
y=y0[index]
z=z0[index]
#Extract QTN
QTN=GI.MP[which(GI.MP[,borrowSlot]==1),]
#print(QTN)
#Draw circles with same size and different thikness
size=1 #1
ratio=10 #5
base=1 #1
themax=ceiling(max(y))
themin=floor(min(y))
wd=((y-themin+base)/(themax-themin+base))*size*ratio
s=size-wd/ratio/2
#print("Manhattan XY created")
####xiaolei update on 2016/01/09
if(plot.style =="FarmCPU"){
pdf(paste("FarmCPU.", name.of.trait,".Manhattan.Plot.Genomewise.pdf" ,sep = ""), width = 13,height=5.75)
}else{
pdf(paste("GAPIT.", name.of.trait,".Manhattan.Plot.Genomewise.pdf" ,sep = ""), width = 13,height=5.75)
}
par(mar = c(3,6,5,1))
plot(y~x,xlab="",ylab=expression(-log[10](italic(p))) ,
cex.axis=1.5, cex.lab=2, ,col=plot.color[z],axes=FALSE,type = "p",pch=mypch,lwd=wd,cex=s+.3,main = paste(name.of.trait,sep=" "),cex.main=2.5)
#Label QTN positions
if(is.vector(QTN)){
if(position.only){abline(v=QTN[2], lty = 2, lwd=1.5, col = "grey")}else{
points(QTN[2], QTN[3], type="p",pch=21, cex=2,lwd=1.5,col="dimgrey")
points(QTN[2], QTN[3], type="p",pch=20, cex=1,lwd=1.5,col="dimgrey")
}
}else{
if(position.only){abline(v=QTN[,2], lty = 2, lwd=1.5, col = "grey")}else{
points(QTN[,2], QTN[,3], type="p",pch=21, cex=2,lwd=1.5,col="dimgrey")
points(QTN[,2], QTN[,3], type="p",pch=20, cex=1,lwd=1.5,col="dimgrey")
}
}
#Add a horizontal line for bonferroniCutOff
abline(h=bonferroniCutOff,col="forestgreen")
#print(bonferroniCutOff)
#Set axises
# jiabo creat chor_taxa
#print(chor_taxa)
if(length(chor_taxa)!=length(ticks))chor_taxa=NULL
#print(unique(GI.MP[,1]))
if(!is.null(chor_taxa))
{axis(1, at=ticks,cex.axis=1.5,labels=chor_taxa,tick=F)
}else{axis(1, at=ticks,cex.axis=1.5,labels=chm.to.analyze,tick=F)}
axis(2, at=1:themax,cex.axis=1.5,labels=1:themax,tick=F)
box()
palette("default")
dev.off()
#print("Manhattan done Genomewise")
} #Genomewise plot
print("GAPIT.Manhattan accomplished successfully!zw")
} #end of GAPIT.Manhattan
#=============================================================================================
`GAPIT.Memory.Object` <-
function(name.of.trait="Trait"){
# Object: To report memoery usage
# Authors: Heuristic Andrew
# http://heuristically.wordpress.com/2010/01/04/r-memory-usage-statistics-variable/
# Modified by Zhiwu Zhang
# Last update: may 29, 2011
##############################################################################################
# print aggregate memory usage statistics
print(paste('R is using', memory.size(), 'MB out of limit', memory.limit(), 'MB'))
# create function to return matrix of memory consumption
object.sizes <- function()
{
return(rev(sort(sapply(ls(envir=.GlobalEnv), function (object.name)
object.size(get(object.name))))))
}
# export file in table format
memory=object.sizes()
file=paste("GAPIT.", name.of.trait,".Memory.Object.csv" ,sep = "")
write.table(memory, file, quote = FALSE, sep = ",", row.names = TRUE,col.names = TRUE)
# export file in PDF format
pdf(paste("GAPIT.", name.of.trait,".Memory.Object.pdf" ,sep = ""))
# draw bar plot
barplot(object.sizes(),
main="Memory usage by object", ylab="Bytes", xlab="Variable name",
col=heat.colors(length(object.sizes())))
# draw dot chart
dotchart(object.sizes(), main="Memory usage by object", xlab="Bytes")
# draw pie chart
pie(object.sizes(), main="Memory usage by object")
dev.off()
}
#=============================================================================================
`GAPIT.Memory` <-
function(Memory =NULL,Infor){
#Object: To report memory usage
#Output: Memory
#Authors: Zhiwu Zhang
# Last update: June 6, 2011
##############################################################################################
gc()
size <- memory.size()
#print(paste("Memory usage: ",size," for", Infor))
if(is.null(Memory)) {
Increased=0
Memory =cbind(Infor,size ,Increased)
}else{
Increased=0
Memory.current=cbind(Infor,size ,Increased)
Memory=rbind(Memory,Memory.current)
Memory[nrow(Memory),3]=as.numeric(as.matrix(Memory[nrow(Memory),2]))-as.numeric(as.matrix(Memory[nrow(Memory)-1,2]))
}
return (Memory)
}#end of GAPIT.Memory function
#=============================================================================================
`GAPIT.Multiple.Manhattan` <-
function(model_store,DPP=50000,cutOff=0.01,band=5,seqQTN=NULL,Y=NULL,GM=NULL,interQTN=NULL,plot.style="Oceanic",plot.line=FALSE){
#Object: Make a Manhattan Plot
#Options for plot.type = "Separate_Graph_for_Each_Chromosome" and "Same_Graph_for_Each_Chromosome"
#Output: A pdf of the Manhattan Plot
#Authors: Alex Lipka, Zhiwu Zhang, Meng Li and Jiabo Wang
# Last update: Oct 10, 2016
#Add r2 between candidata SNP and other markers in on choromosome
##############################################################################################
Nenviron=length(model_store)*(ncol(Y)-1)
environ_name=NULL
new_xz=NULL
for(i in 1:length(model_store))
{
for(j in 1:(ncol(Y)-1))
{
environ_name=c(environ_name,paste(model_store[i],".",colnames(Y)[-1][j],sep=""))
}
}
sig_pos=NULL
simulation=FALSE
if(!is.null(seqQTN)){
#seqQTN=-seqQTN
simulation=TRUE
}
for(i in 1:length(environ_name))
{
environ_result=read.csv(paste("GAPIT.",environ_name[i],".GWAS.Results.csv",sep=""),head=T)
environ_filter=environ_result[!is.na(environ_result[,4]),]
y_filter=environ_filter[environ_filter[,4]<(cutOff/(nrow(environ_filter))),]
write.table(y_filter,paste("Filter_",environ_name[i],"_GWAS_result.txt",sep=""))
result=environ_result[,1:4]
result=result[match(as.character(GM[,1]),as.character(result[,1])),]
# result=result[order(result[,2]),]
# result=result[order(result[,1]),]
#print(head(result))
rownames(result)=1:nrow(result)
#print(i)
if(i==1){
result0=result
colnames(result0)[4]=environ_name[i]
}
if(i!=1){
result0=merge(result0,result[,c(1,4)],by.x=colnames(result0)[1],by.y=colnames(result)[1])
colnames(result0)[i+3]=environ_name[i]
}
rownames(result)=1:nrow(result)
result[is.na(result[,4]),4]=1
sig_pos=append(sig_pos,as.numeric(rownames(result[result[!is.na(result[,4]),4]<(cutOff/nrow(result)),])))
}
#if(length(sig_pos)!=0)sig_pos=sig_pos[!duplicated(sig_pos)]
if(length(sig_pos[!is.na(sig_pos)])!=0)
{ x_matrix=as.matrix(table(sig_pos))
x_matrix=cbind(as.data.frame(rownames(x_matrix)),x_matrix)
#print(x_matrix)
lastbase=0
map_store=as.matrix(cbind(as.numeric(GM[,2]),as.numeric(as.vector(GM[,3]))))
#print(head(map_store))
#print(as.numeric(map_store[,3]))
for (j in unique(map_store[,1]))
{
index=map_store[,1]==j
#print(table(index))
map_store[index,2]=as.numeric(map_store[index,2])+lastbase
lastbase=max(as.numeric(map_store[index,2]))
#print(lastbase)
}
colnames(x_matrix)=c("pos","times")
#colnames(xz)=c("pos","col")
new_xz=cbind(x_matrix,map_store[as.numeric(as.character(x_matrix[,1])),])
#new_xz[,4]=0
colnames(new_xz)=c("pos","times","chro","xlab")
new_xz=new_xz[!duplicated(new_xz),]
new_xz[new_xz[,2]>=3,2]=3
new_xz[,2]=4-new_xz[,2]
new_xz[new_xz[,2]==3,2]=0
new_xz=as.matrix(new_xz)
new_xz=new_xz[new_xz[,2]!="0",]
new_xz=matrix(new_xz,length(as.vector(new_xz))/4,4)
#print(new_xz)
plot.line=TRUE
#print(new_xz)
}
#print(as.numeric(new_xz[,4]))
#print(head(result0))
# print(as.numeric(new_xz[,1]))
pdf(paste("GAPIT.Manhattan.Mutiple.Plot",colnames(result0)[-c(1:3)],".pdf" ,sep = ""), width = 20,height=6*Nenviron)
par(mfrow=c(Nenviron,1))
for(k in 1:Nenviron)
{ if(k==Nenviron){#par(mfrow=c(Nenviron,1))
par(mar = c(3,8,1,8))
}else{
#par(mfrow=c(Nenviron,1))
par(mar = c(0,8,1,8))
}
environ_result=read.csv(paste("GAPIT.",environ_name[k],".GWAS.Results.csv",sep=""),head=T)
#print(environ_result[as.numeric(new_xz[,1]),])
result=environ_result[,1:4]
result=result[match(as.character(GM[,1]),as.character(result[,1])),]
rownames(result)=1:nrow(result)
GI.MP=result[,c(2:4)]
borrowSlot=4
GI.MP[,borrowSlot]=0 #Inicial as 0
GI.MP[,5]=1:(nrow(GI.MP))
GI.MP[,6]=1:(nrow(GI.MP))
GI.MP <- GI.MP[!is.na(GI.MP[,1]),]
GI.MP <- GI.MP[!is.na(GI.MP[,2]),]
GI.MP[is.na(GI.MP[,3]),3]=1
#Retain SNPs that have P values between 0 and 1 (not na etc)
GI.MP <- GI.MP[GI.MP[,3]>0,]
GI.MP <- GI.MP[GI.MP[,3]<=1,]
#Remove chr 0 and 99
GI.MP <- GI.MP[GI.MP[,1]!=0,]
total_chromo=max(GI.MP[,1])
# print(dim(GI.MP))
if(!is.null(seqQTN))GI.MP[seqQTN,borrowSlot]=1
numMarker=nrow(GI.MP)
bonferroniCutOff=-log10(cutOff/numMarker)
GI.MP[,3] <- -log10(GI.MP[,3])
GI.MP[,5]=1:numMarker
y.lim <- ceiling(max(GI.MP[,3]))
chm.to.analyze <- unique(GI.MP[,1])
chm.to.analyze=chm.to.analyze[order(chm.to.analyze)]
nchr=length(chm.to.analyze)
GI.MP[,6]=1:(nrow(GI.MP))
MP_store=GI.MP
index_GI=MP_store[,3]>=0
MP_store <- MP_store[index_GI,]
ticks=NULL
lastbase=0
for (i in chm.to.analyze)
{
index=(MP_store[,1]==i)
ticks <- c(ticks, lastbase+mean(MP_store[index,2]))
MP_store[index,2]=MP_store[index,2]+lastbase
lastbase=max(MP_store[index,2])
}
x0 <- as.numeric(MP_store[,2])
y0 <- as.numeric(MP_store[,3])
z0 <- as.numeric(MP_store[,1])
x1=sort(x0)
position=order(y0,decreasing = TRUE)
values=y0[position]
if(length(values)<=DPP)
{
index=position[c(1:length(values))]
}else{
values=sqrt(values) #This shift the weight a little bit to the low building.
#Handler of bias plot
rv=runif(length(values))
values=values+rv
values=values[order(values,decreasing = T)]
theMin=min(values)
theMax=max(values)
range=theMax-theMin
interval=range/DPP
ladder=round(values/interval)
ladder2=c(ladder[-1],0)
keep=ladder-ladder2
index=position[which(keep>=0)]
}
x=x0[index]
y=y0[index]
z=z0[index]
# print(length(x))
#Extract QTN
#if(!is.null(seqQTN))MP_store[seqQTN,borrowSlot]=1
#if(!is.null(interQTN))MP_store[interQTN,borrowSlot]=2
QTN=MP_store[which(MP_store[,borrowSlot]==1),]
#Draw circles with same size and different thikness
size=1 #1
ratio=10 #5
base=1 #1
numCHR=nchr
themax=ceiling(max(y))
themin=floor(min(y))
wd=((y-themin+base)/(themax-themin+base))*size*ratio
s=size-wd/ratio/2
ncycle=ceiling(nchr/5)
ncolor=5*ncycle
ncolor=band*ncycle
thecolor=seq(1,nchr,by= ncycle)
mypch=1
#plot.color= rainbow(ncolor+1)
col.Rainbow=rainbow(ncolor+1)
col.FarmCPU=rep(c("#CC6600","deepskyblue","orange","forestgreen","indianred3"),ceiling(numCHR/5))
col.Rushville=rep(c("orangered","navyblue"),ceiling(numCHR/2))
col.Congress=rep(c("deepskyblue3","firebrick"),ceiling(numCHR/2))
col.Ocean=rep(c("steelblue4","cyan3"),ceiling(numCHR/2))
col.PLINK=rep(c("gray10","gray70"),ceiling(numCHR/2))
col.Beach=rep(c("turquoise4","indianred3","darkolivegreen3","red","aquamarine3","darkgoldenrod"),ceiling(numCHR/5))
#col.Oceanic=rep(c( '#EC5f67', '#F99157', '#FAC863', '#99C794', '#5FB3B3', '#6699CC', '#C594C5', '#AB7967'),ceiling(numCHR/8))
#col.Oceanic=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5', '#AB7967'),ceiling(numCHR/6))
col.Oceanic=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(numCHR/5))
col.cougars=rep(c( '#990000', 'dimgray'),ceiling(numCHR/2))
if(plot.style=="Rainbow")plot.color= col.Rainbow
if(plot.style =="FarmCPU")plot.color= col.Rainbow
if(plot.style =="Rushville")plot.color= col.Rushville
if(plot.style =="Congress")plot.color= col.Congress
if(plot.style =="Ocean")plot.color= col.Ocean
if(plot.style =="PLINK")plot.color= col.PLINK
if(plot.style =="Beach")plot.color= col.Beach
if(plot.style =="Oceanic")plot.color= col.Oceanic
if(plot.style =="cougars")plot.color= col.cougars
#plot.color=rep(c( '#EC5f67', '#FAC863', '#99C794', '#6699CC', '#C594C5'),ceiling(ncolor/5))
plot(y~x,xlab="",ylab="" ,ylim=c(0,themax),
cex.axis=4, cex.lab=4, ,col=plot.color[z],axes=FALSE,type = "p",pch=mypch,lwd=wd,cex=s+2.5,cex.main=4)
mtext(side=2,expression(-log[10](italic(p))),line=3, cex=2.5)
#Label QTN positions
#print(head(QTN))
#print(head(interQTN))
if(!simulation){abline(v=QTN[2], lty = 2, lwd=1.5, col = "grey")}else{
#print("$$$$$$")
points(QTN[,2], QTN[,3], pch=20, cex=2.5,lwd=2.5,col="black")
#points(interQTN[,2], interQTN[,3], type="p",pch=8, cex=1,lwd=1.5,col="dimgrey")
}
#}
if(plot.line){
#print(x)
#print(as.numeric(new_xz[,2]))
# if(!is.null(nrow(new_xz))) {abline(v=as.numeric(new_xz[,4]),col=plot.color[as.numeric(new_xz[,3])],lty=as.numeric(new_xz[,2]),untf=T,lwd=3)
if(!is.null(nrow(new_xz))) {abline(v=as.numeric(new_xz[,4]),col="grey",lty=as.numeric(new_xz[,2]),untf=T,lwd=3)
}else{abline(v=as.numeric(new_xz[1]),col=plot.color[as.numeric(new_xz[3])],lty=as.numeric(new_xz[2]),untf=T,lwd=3)
}
}
#Add a horizontal line for bonferroniCutOff
abline(h=bonferroniCutOff,lty=2,untf=T,lwd=3,col="red")
axis(2, xaxp=c(1,themax,5),cex.axis=2.5,tick=F)
if(k==Nenviron)axis(1, at=ticks,cex.axis=2.7,labels=chm.to.analyze,tick=F)
mtext(side=4,paste(environ_name[k],sep=""),line=3,cex=2.5)
box()
}#end of environ_name
dev.off()
print("GAPIT.Manhattan.Mutiple.Plot has done !!!")
return(list(multip_mapP=result0,xz=new_xz))
} #end of GAPIT.Manhattan
#=============================================================================================
`GAPIT.Numericalization` <-
function(x,bit=2,effect="Add",impute="None", Create.indicator = FALSE, Major.allele.zero = FALSE, byRow=TRUE){
#Object: To convert character SNP genotpe to numerical
#Output: Coresponding numerical value
#Authors: Feng Tian and Zhiwu Zhang
# Last update: May 30, 2011
##############################################################################################
if(bit==1) {
x[x=="X"]="N"
x[x=="-"]="N"
x[x=="+"]="N"
x[x=="/"]="N"
x[x=="K"]="Z" #K (for GT genotype)is replaced by Z to ensure heterozygose has the largest value
}
if(bit==2) {
x[x=="XX"]="N"
x[x=="--"]="N"
x[x=="++"]="N"
x[x=="//"]="N"
x[x=="NN"]="N"
x[x=="00"]="N"
}
n=length(x)
lev=levels(as.factor(x))
lev=setdiff(lev,"N")
#print(lev)
len=length(lev)
#print(len)
#Jiabo creat this code to convert AT TT to 1 and 2. 2018.5.29
if(bit==2)
{
inter_store=c("AT","AG","AC","TA","GA","CA","GT","TG","GC","CG","CT","TC")
inter=intersect(lev,inter_store)
if(length(inter)>1)
{
x[x==inter[2]]=inter[1]
n=length(x)
lev=levels(as.factor(x))
lev=setdiff(lev,"N")
#print(lev)
len=length(lev)
}
if(len==2&bit==2)
{ #inter=intersect(lev,inter_store)
if(!is.na(inter[1]))
{
lev=union(lev,"UU")
len=len+1
}
}
if(len==3&bit==2)
{
inter=intersect(lev,inter_store)
}
}
#print(lev)
#print(len)
#Jiabo code is end here
#Genotype counts
count=1:len
for(i in 1:len){
count[i]=length(x[(x==lev[i])])
}
#print(count)
if(Major.allele.zero){
if(len>1 & len<=3){
#One bit: Make sure that the SNP with the major allele is on the top, and the SNP with the minor allele is on the second position
if(bit==1){
count.temp = cbind(count, seq(1:len))
if(len==3) count.temp = count.temp[-3,]
count.temp <- count.temp[order(count.temp[,1], decreasing = TRUE),]
if(len==3)order = c(count.temp[,2],3)else order = count.temp[,2]
}
#Two bit: Make sure that the SNP with the major allele is on the top, and the SNP with the minor allele is on the third position
if(bit==2){
count.temp = cbind(count, seq(1:len))
if(len==3) count.temp = count.temp[-2,]
count.temp <- count.temp[order(count.temp[,1], decreasing = TRUE),]
if(len==3) order = c(count.temp[1,2],2,count.temp[2,2])else order = count.temp[,2]
}
count = count[order]
lev = lev[order]
} #End if(len<=1 | len> 3)
} #End if(Major.allele.zero)
#print(x)
#make two bit order genotype as AA,AT and TT, one bit as A(AA),T(TT) and X(AT)
if(bit==1 & len==3){
temp=count[2]
count[2]=count[3]
count[3]=temp
}
#print(lev)
#print(count)
position=order(count)
#Jiabo creat this code to convert AT TT to 1 and 2.2018.5.29
lev1=lev
if(bit==2&len==3)
{
lev1[1]=lev[count==sort(count)[1]]
lev1[2]=lev[count==sort(count)[2]]
lev1[3]=lev[count==sort(count)[3]]
position=c(1:3)
lev=lev1
}
#print(lev)
#print(position)
#print(inter)
#Jiabo code is end here
#1status other than 2 or 3
if(len<=1 | len> 3)x=0
#2 status
if(len==2)x=ifelse(x=="N",NA,ifelse(x==lev[1],0,2))
#3 status
if(bit==1){
if(len==3)x=ifelse(x=="N",NA,ifelse(x==lev[1],0,ifelse(x==lev[3],1,2)))
}else{
if(len==3)x=ifelse(x=="N",NA,ifelse(x==lev[lev!=inter][1],0,ifelse(x==inter,1,2)))
}
#print(paste(lev,len,sep=" "))
#print(position)
#missing data imputation
if(impute=="Middle") {x[is.na(x)]=1 }
if(len==3){
if(impute=="Minor") {x[is.na(x)]=position[1] -1}
if(impute=="Major") {x[is.na(x)]=position[len]-1}
}else{
if(impute=="Minor") {x[is.na(x)]=2*(position[1] -1)}
if(impute=="Major") {x[is.na(x)]=2*(position[len]-1)}
}
#alternative genetic models
if(effect=="Dom") x=ifelse(x==1,1,0)
if(effect=="Left") x[x==1]=0
if(effect=="Right") x[x==1]=2
if(byRow) {
result=matrix(x,n,1)
}else{
result=matrix(x,1,n)
}
return(result)
}#end of GAPIT.Numericalization function
#=============================================================================================
`GAPIT.PCA` <-
function(X,taxa, PC.number = min(ncol(X),nrow(X)),file.output=TRUE,PCA.total=0,PCA.col=NULL,PCA.3d=FALSE){
# Object: Conduct a principal component analysis, and output the prinicpal components into the workspace,
# a text file of the principal components, and a pdf of the scree plot
# Authors: Alex Lipka and Hyun Min Kang
# Last update: May 31, 2011
##############################################################################################
#Conduct the PCA
print("Calling prcomp...")
PCA.X <- prcomp(X)
eigenvalues <- PCA.X$sdev^2
evp=eigenvalues/sum(eigenvalues)
nout=min(10,length(evp))
xout=1:nout
if(is.null(PCA.col)) PCA.col="red"
print("Creating PCA graphs...")
#Create a Scree plot
if(file.output & PC.number>1) {
pdf("GAPIT.PCA.eigenValue.pdf", width = 12, height = 12)
par(mar=c(5,5,4,5)+.1,cex=2)
#par(mar=c(10,9,9,10)+.1)
plot(xout,eigenvalues[xout],type="b",col="blue",xlab="Principal components",ylab="Variance")
par(new=TRUE)
plot(xout,evp[xout]*100,type="n",col="red",xaxt="n",yaxt="n",xlab="",ylab="")
axis(4)
mtext("Percentage (%)",side=4,line=3,cex=2)
dev.off()
pdf("GAPIT.PCA.2D.pdf", width = 8, height = 8)
par(mar = c(5,5,5,5))
maxPlot=min(as.numeric(PC.number[1]),3)
for(i in 1:(maxPlot-1)){
for(j in (i+1):(maxPlot)){
plot(PCA.X$x[,i],PCA.X$x[,j],xlab=paste("PC",i,sep=""),ylab=paste("PC",j,sep=""),pch=19,col=PCA.col,cex.axis=1.3,cex.lab=1.4, cex.axis=1.2, lwd=2,las=1)
}
}
dev.off()
#output 3D plot
if(PCA.3d==TRUE)
{
if(1>2)
{if(!require(lattice)) install.packages("lattice")
library(lattice)
pca=as.data.frame(PCA.X$x)
png(file="example%03d.png", width=500, heigh=500)
for (i in seq(10, 80 , 1)){
print(cloud(PC1~PC2*PC3,data=pca,screen=list(x=i,y=i-40),pch=20,color="red",
col.axis="blue",cex=1,cex.lab=1.4, cex.axis=1.2,lwd=3))
}
dev.off()
system("convert -delay 40 *.png GAPIT.PCA.3D.gif")
# cleaning up
file.remove(list.files(pattern=".png"))
}
if(!require(rgl)) install.packages("rgl")
if(!require(rglwidget)) install.packages("rglwidget")
library(rgl)
PCA1 <- PCA.X$x[,1]
PCA2 <- PCA.X$x[,2]
PCA3 <- PCA.X$x[,3]
plot3d(PCA1, PCA2, PCA3, col = "white",radius=0.01)
num_col=length(unique(PCA.col))
if(num_col==1)
{
sids1 <- spheres3d(PCA1, PCA2, PCA3, col = PCA.col,radius=1)
widgets<-rglwidget(width = 900, height = 900) %>%toggleWidget(ids = sids1, label = "PCA")
}else if(num_col==2)
{
index1=PCA.col==unique(PCA.col)[1]
index2=PCA.col==unique(PCA.col)[2]
sids1 <- spheres3d(PCA1[index1], PCA2[index1], PCA3[index1], col = PCA.col[index1],radius=1)
sids2 <- spheres3d(PCA1[index2], PCA2[index2], PCA3[index2], col = PCA.col[index2],radius=1)
widgets<-rglwidget(width = 900, height = 900) %>%toggleWidget(ids = sids1, label = "Population 1")%>%toggleWidget(ids = sids2, label = "Population 2")
}else if(num_col==3)
{
index1=PCA.col==unique(PCA.col)[1]
index2=PCA.col==unique(PCA.col)[2]
index3=PCA.col==unique(PCA.col)[3]
sids1 <- spheres3d(PCA1[index1], PCA2[index1], PCA3[index1], col = PCA.col[index1],radius=1)
sids2 <- spheres3d(PCA1[index2], PCA2[index2], PCA3[index2], col = PCA.col[index2],radius=1)
sids3 <- spheres3d(PCA1[index3], PCA2[index3], PCA3[index3], col = PCA.col[index3],radius=1)
widgets<-rglwidget(width = 900, height = 900) %>%toggleWidget(ids = sids1, label = "Population 1")%>%toggleWidget(ids = sids2, label = "Population 2")%>%toggleWidget(ids = sids3, label = "Population 3")
}else if(num_col==4)
{
index1=PCA.col==unique(PCA.col)[1]
index2=PCA.col==unique(PCA.col)[2]
index3=PCA.col==unique(PCA.col)[3]
index4=PCA.col==unique(PCA.col)[4]
sids1 <- spheres3d(PCA1[index1], PCA2[index1], PCA3[index1], col = PCA.col[index1],radius=1)
sids2 <- spheres3d(PCA1[index2], PCA2[index2], PCA3[index2], col = PCA.col[index2],radius=1)
sids3 <- spheres3d(PCA1[index3], PCA2[index3], PCA3[index3], col = PCA.col[index3],radius=1)
sids4 <- spheres3d(PCA1[index4], PCA2[index4], PCA3[index4], col = PCA.col[index4],radius=1)
widgets<-rglwidget(width = 900, height = 900) %>%toggleWidget(ids = sids1, label = "Population 1")%>%toggleWidget(ids = sids2, label = "Population 2")%>%toggleWidget(ids = sids3, label = "Population 3")%>%toggleWidget(ids = sids4, label = "Population 4")
}
if (interactive()) widgets
htmltools::save_html(widgets, "Interactive.PCA.html")
}
if(!require(scatterplot3d)) install.packages("scatterplot3d")
library(scatterplot3d)
pdf("GAPIT.PCA.3D.pdf", width = 7, height = 7)
par(mar = c(5,5,5,5))
scatterplot3d(PCA.X$x[,1],PCA.X$x[,2],PCA.X$x[,3],xlab=paste("PC",1,sep=""),ylab=paste("PC",2,sep=""),zlab=paste("PC",3,sep="") ,pch=20,color=PCA.col,col.axis="blue",cex=1,cex.lab=1.4, cex.axis=1.2,lwd=3,angle=55,scale.y=0.7)
dev.off()
}
print("Joining taxa...")
#Extract number of PCs needed
PCs <- cbind(taxa,as.data.frame(PCA.X$x))
#Remove duplicate (This is taken care by QC)
#PCs.unique <- unique(PCs[,1])
#PCs <-PCs[match(PCs.unique, PCs[,1], nomatch = 0), ]
print("Exporting PCs...")
#Write the PCs into a text file
if(file.output) write.table(PCs[,1:(PCA.total+1)], "GAPIT.PCA.csv", quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
if(file.output) write.table(PCA.X$rotation[,1:PC.number], "GAPIT.PCA.loadings.csv", quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
if(file.output) write.table(eigenvalues, "GAPIT.PCA.eigenvalues.csv", quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#Return the PCs
return(list(PCs=PCs,EV=PCA.X$sdev^2,nPCs=NULL))
}
#=============================================================================================
`GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure` <-
function(PWI = PWI, FDR.Rate = 0.05, FDR.Procedure = "BH"){
#Object: Conduct the Benjamini-Hochberg FDR-Controlling Procedure
#Output: PWIP, number.of.significant.SNPs
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: May 5, 2011
##############################################################################################
#Make sure that your compouter has the latest version of Bioconductor (the "Biobase" package) and multtest
if(is.null(PWI))
{
PWIP=NULL
number.of.significant.SNPs = 0
}
if(!is.null(PWI))
{
#library(multtest)
if(dim(PWI)[1] == 1){
PWIP <- cbind(PWI, PWI[4])
colnames(PWIP)[9] <- "FDR_Adjusted_P-values"
}
if(dim(PWI)[1] > 1){
#mt.rawp2adjp Performs the Simes procedure. The output should be two columns, Left column: originial p-value
#Right column: Simes corrected p-value
res <- mt.rawp2adjp(PWI[,4], FDR.Procedure)
#This command should order the p-values in the order of the SNPs in the data set
adjp <- res$adjp[order(res$index), ]
#round(adjp[1:7,],4)
#Logical statment: 0, if Ho is not rejected; 1, if Ho is rejected, by the Simes corrected p-value
# temp <- mt.reject(adjp[,2], FDR.Rate)
#Lists all number of SNPs that were rejected by the BY procedure
#temp$r
#Attach the FDR adjusted p-values to AS_Results
PWIP <- cbind(PWI, adjp[,2])
#Sort these data by lowest to highest FDR adjusted p-value
PWIP <- PWIP[order(PWIP[,4]),]
colnames(PWIP)[9] <- "FDR_Adjusted_P-values"
# number.of.significant.SNPs = temp$r
}
#print("GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure accomplished successfully!")
}
#return(list(PWIP=PWIP, number.of.significant.SNPs = number.of.significant.SNPs))
return(list(PWIP=PWIP))
}#GAPIT.Perform.BH.FDR.Multiple.Correction.Procedure ends here
#=============================================================================================
`GAPIT.Phenotype.PCA.View` <-function(PC=NULL,myY=NULL){
# Object: Analysis PCA effection for Phenotype data ,result:a pdf of the scree plot
# myG:Genotype data
# myY:Phenotype data
# Authors: You Tang
# Last update: Sep 7, 2015
##############################################################################################
print("GAPIT.Phenotype.PCA.View")
if(is.null(PC)){stop("Validation Invalid. Please input four PC value !")}
if(is.null(myY)){stop("Validation Invalid. Please select read valid Phenotype flies !")}
y<-myY[!is.na(myY[,2]),c(1:2)]
traitname=colnames(y)[2]
cv1<-PC[!is.na(match(PC[,1],y[,1])),]
y1<-y[!is.na(match(y[,1],cv1[,1])),]
y2<-y1[order(y1[,1]),]
cv2<-cv1[order(cv1[,1]),]
lcor=round(cor(y2[,-1],cv2[,-1])*100)/100
y.range=max(y2[,2])-min(y2[,2])
y.mean=mean(y2[,2])
n.col=54
y.int=round(abs(y2[,2]-y.mean)/y.range*(.5*n.col-1)*2)+1
mycol=rainbow(n.col)
y.col=mycol[y.int]
y.lab=paste("PC",seq(1:4)," (r=",lcor,")",sep="")
pdf(paste("GAPIT.",traitname,"_vs_PC.pdf",sep=""), width =9, height = 6)
#par(mar = c(5,5,5,5))
par(mar = c(5,5,2,2))
par(mfrow=c(2,2))
plot(y2[,2],cv2[,2],bg="lightgray",xlab="Phenotype",ylab=y.lab[1],main="",cex.lab=1.4,col=y.col)
if(ncol(PC)>2) plot(y2[,2],cv2[,3],bg="lightgray",xlab="Phenotype",ylab=y.lab[2],main="",cex.lab=1.4,col=y.col)
if(ncol(PC)>3) plot(y2[,2],cv2[,4],bg="lightgray",xlab="Phenotype",ylab=y.lab[3],main="",cex.lab=1.4,col=y.col)
if(ncol(PC)>4) plot(y2[,2],cv2[,5],bg="lightgray",xlab="Phenotype",ylab=y.lab[4],main="",cex.lab=1.4,col=y.col)
dev.off()
print(paste("GAPIT.Phenotype.PCA.View ", ".output pdf generate.","successfully!" ,sep = ""))
#GAPIT.Phenotype.View
}
#=============================================================================================
`GAPIT.Phenotype.Simulation` <-
function(GD,GM=NULL,h2=.75,NQTN=10,QTNDist="normal",effectunit=1,category=1,r=0.25,CV,cveff=NULL,a2=0,adim=2){
#Object: To simulate phenotype from genotye
#Input: GD - n by m +1 dataframe or n by m big.matrix
#intput: h2 - heritability
#intput: NQTN - number of QTNs
#intput: QTNDist - Distribution of QTN, options are "geometry", "normal"
#intput: effectunit - effect of fitst QTN, the nect effect is its squre
#intput: theSeed - seed for randomization
#Output: Y,U,E,QTN.Position, and effect
#Straitegy: NA
#Authors: Qishan Wang and Zhiwu Zhang
#Start date: April 4, 2013
#Last update: April 4, 2013
#Set orientation
#Strategy: the number of rows in GD and GM are the same if GD has SNP as row
##############################################################################################
#print("GAPIT.Phenotype.Simulation")
nm=ncol(GD)-1 #Initial by assume GD has snp in col
if(!is.null(GM)) nm=nrow(GM)
ngd1=nrow(GD)
ngd2=ncol(GD)
ngd1=abs(ngd1-nm)
ngd2=abs(ngd2-nm)
orientation="row"
ns=ncol(GD)
if(min(ngd1,ngd2)>0){
orientation="col"
ns=nrow(GD)
}
n= ns #number of samples
m=nm #number of markers
#Set QTN effects
if (QTNDist=="normal"){ addeffect<-rnorm(NQTN,0,1)
}else
{addeffect=effectunit^(1:NQTN)}
#Simulating Genetic effect
#r=sample(2:m,NQTN,replace=F)
QTN.position=sample(1:m,NQTN,replace=F)
if(orientation=="col") SNPQ=as.matrix(GD[,(QTN.position+1)])
if(orientation=="row") SNPQ=t(as.matrix(GD[QTN.position,]))
#Replace non-variant QTNs (does not work yet)
#inComplete=TRUE
#while(inComplete){
# inComplete=FALSE
# myVar=apply(SNPQ,2,var)
# index=which(myVar==0)
# nInVar=length(index)
# if(nInVar>0){
# inComplete=TRUE
# New.position=sample(1:m,nInVar,replace=F)
# if(orientation=="col") SNPQ[,index]=as.matrix(GD[,(New.position+1)])
# if(orientation=="row") SNPQ[,index]=t(as.matrix(GD[New.position,]))
# }
#}#end of while
effect=SNPQ%*%addeffect
effectvar=var(effect)
#Interaction
cp=0*effect
nint= adim
if(a2>0&NQTN>=nint){
for(i in nint:nint){
Int.position=sample(NQTN,i,replace=F)
cp=apply(SNPQ[,Int.position],1,prod)
}
cpvar=var(cp)
intvar=(effectvar-a2*effectvar)/a2
if(is.na(cp[1]))stop("something wrong in simulating interaction")
if(cpvar>0){
#print(c(effectvar,intvar,cpvar,var(cp),a2))
#print(dim(cp))
cp=cp/sqrt(cpvar)
cp=cp*sqrt(intvar)
effectvar=effectvar+intvar
}else{cp=0*effect}
}
#Residual variance
if(h2 >0){
residualvar=(effectvar-h2*effectvar)/h2
}else{
residualvar=1
effect= effect*0
}
#Variance explained by each SNP
effectInd=SNPQ%*%diag(addeffect)
varInd=apply(effectInd,2,var)
effectSeq=order(varInd,decreasing = TRUE)
#Simulating Residual and phenotype
residual=rnorm(n,0,sqrt(residualvar))
#environment effect
if(!is.null(cveff)){
#print(cveff)
vy=effectvar+residualvar
#print(vy)
ev=cveff*vy/(1-cveff)
ec=sqrt(ev)/sqrt(diag(var(CV[,-1])))
enveff=as.matrix(myCV[,-1])%*%ec
#print(cbind(effectvar,residualvar,ev,ec))
#print(cbind(effect,enveff,residual))
residual=residual+enveff
}
#Simulating phenotype
y=effect+residual+cp
if(orientation=="col") myY=cbind(as.data.frame(GD[,1]),as.data.frame(y))
if(orientation=="row") myY=cbind(NA,as.data.frame(y))
#Convert to category phenotype
if(category>1){
myQuantile =(0:category)/category
y.num= myY[,2]
cutoff=quantile(y.num, myQuantile)
y.cat= .bincode(y.num,cutoff,include.lowest = T)
myY[,2]=y.cat
}
#Binary phenotype
if(category==0){
#Standardization
#print("Binary phenotype")
#print(mean(effect))
#print(sqrt(effectvar))
#print(dim(effect))
x=(effect-mean(effect))
x=x/as.numeric(sqrt(effectvar))
myF=GAPIT.BIPH(x,h2=h2,r=r)
p=runif(n)
index=p<myF
myY[index,2]=1
myY[!index,2]=0
}
#print("Phenotype simulation accoplished")
return(list(Y=myY,u=effect,i=cp,e=residual,QTN.position=QTN.position,effect=addeffect))
} #enf of phenotype simulation function
#=============================================================================================
`GAPIT.Phenotype.View` <-function(myY=NULL,traitname="_",memo="_"){
# Object: Analysis for Phenotype data:Distribution of density,Accumulation,result:a pdf of the scree plot
# myY:Phenotype data
# Authors: You Tang
# Last update: Sep 7, 2015
##############################################################################################
print("GAPIT.Phenotype.View in press...")
if(is.null(myY)){stop("Validation Invalid. Please select read valid Phenotype flies !")}
y<-myY[!is.na(myY[,2]),2]
obs<-as.matrix(y)
traitname=colnames(myY)[2]
pdf(paste("GAPIT",memo,traitname,"phenotype_view.pdf",sep ="."), width =10, height = 6)
par(mar = c(5,5,5,5))
par(mfrow=c(2,2))
plot(obs,pch=1)
#hist(obs)
hist(obs,xlab="Density",main="",breaks=12, cex.axis=1,col = "gray")
boxplot(obs)
plot(ecdf(obs),col="red",bg="lightgray",xlab="Density",ylab="Accumulation",main="")
dev.off()
print(paste("GAPIT.Phenotype.View ", ".output pdf generate.","successfully!" ,sep = ""))
#GAPIT.Phenotype.View
}
#=============================================================================================
`GAPIT.Power` <-
function(WS=c(1e0,1e3,1e4,1e5,1e6,1e7), GM=NULL,seqQTN=NULL,GWAS=NULL,maxOut=100,
alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),MaxBP=1e10){
#Object: To evaluate power and FDR for the top (maxOut) positive interval defined by WS
#Input: WS- window size
#Input: GM - m by 3 matrix for SNP name, chromosome and BP
#Input: seqQTN - s by 1 vecter for index of QTN on GM (+1 for GDP column wise)
#Input: GWAS- SNP,CHR,BP,P,MAF
#maxOut: maximum number of rows to report
#Requirement: None
#Output: Table and Plots
#Authors: Zhiwu Zhang
# Date start: April 2, 2013
# Last update: April 2, 2013
##############################################################################################
#print("GAPIT.Power Started")
if(is.null(seqQTN) | is.null(GM) | is.null(GWAS)) return(list(FDR=NULL,Power=NULL,Power.Alpha=NULL,alpha=NULL))
#-----------------FDR and Power analysis-------------------------
#Information needed: myGAPIT$GWAS,myGM and QTN(r)
nWin=matrix(NA,length(WS),1)
format_GWAS=cbind(GWAS[,1:4],NA,NA,NA)
names(format_GWAS)<-c("SNP","Chromosome","Position","P.value","maf","nobs","FDR_Adjusted_P-values")
myGM=GM
#loop window size here
theWS=1
for (theWS in 1:length(WS)){
ws=WS[theWS]
#Label QTN intervals
#Restore original order
#QTNList=r-1
QTNList=seqQTN
myGM2=cbind(myGM,rep(0,nrow(myGM)),1:nrow(myGM),NA) #Initial QTN status as 0
#Extract QTN positions
myGM2[,6]=floor((as.numeric(as.character(myGM2[,2]))*MaxBP+as.numeric(as.character(myGM2[,3])))/ws) #Label QTN as 1
QTNInterval=myGM2[QTNList,6]
thePosition=myGM2[,6] %in% QTNInterval
myGM2[thePosition,4]=1 #Label QTN as 1
names(myGM2) <- c("SNP","Chromosome","Position", "QTN","Seq")
#Merge to P vlaues
#GWAS<- merge(myGAPIT$GWAS[,1:7],myGM2[,c(1,4,5)],by="SNP")
GWAS<- merge(format_GWAS[,1:7],myGM2[,c(1,4,5)],by="SNP")#xiaoalei changed
#checking
#zw=GWAS[order(GWAS[,4],decreasing = FALSE),]
#zw=GWAS[order(GWAS[,8],decreasing = TRUE),]
#head(zw)
#Creat windows
myQTN=GAPIT.Specify(GI=GWAS[,1:3],GP=GWAS,bin.size=ws,MaxBP=MaxBP)
QTN=GWAS[myQTN$index,]
#Calculate alpha
qtnLoc=which(QTN[,8]==1) #get the position of QTN
P.QTN=QTN[qtnLoc,4] #p value of QTN
P.marker=QTN[-qtnLoc,4] #p value of non qtn (marker)
cutOff=matrix(quantile(P.marker, alpha,na.rm=TRUE),ncol=1)#xiaoalei changed
myPower.Alpha=apply(cutOff,1,function(x){
Power=length(which(P.QTN<x))/length(P.QTN)
})
#Sort on P
#QTN=QTN[order(as.numeric(as.character(QTN[,3])),decreasing = FALSE),]
#QTN=QTN[order(as.numeric(as.character(QTN[,2])),decreasing = FALSE),]
QTN=QTN[order(as.numeric(as.character(QTN[,4])),decreasing = FALSE),]
names(QTN) <- c("SNP","Chromosome","Position", "P","FDR","Power","Order","QTN","Seq")
#calculate power
QTN[,7]=1:nrow(QTN)
QTN[,5]=cumsum(1-QTN[,8])/QTN[,7] #FDR
QTN[,6]=cumsum(QTN[,8]) /sum(QTN[,8] ) #Power
#Save results
if (theWS==1){
nWin=matrix(NA,length(WS),1)
FDR=array(NA,dim=c(nrow(QTN),length(WS)))
Power=array(NA,dim=c(nrow(QTN),length(WS)))
Power.Alpha=array(NA,dim=c(length(alpha),length(WS)))
}
nWin[theWS]=nrow(QTN)
FDR[1:nWin[theWS],theWS]=QTN[,5]
Power[1:nWin[theWS],theWS]=QTN[,6]
Power.Alpha[,theWS]=myPower.Alpha
}#end of window size loop
nOut=min(maxOut,max(nWin))
index=1:nOut
return(list(FDR=FDR[index,],Power=Power[index,],Power.Alpha=Power.Alpha,alpha=alpha))
}#end of GAPIT.Power
#=============================================================================================
`GAPIT.Power.compare` <-function(myG=NUll,myGD=NULL,myGM=NULL,myKI=NULL,myY=NULL,myCV=NULL,rel=NULL,h2=NULL,NQTN=NULL){
# Object: compare to Power against FDR for GLM,MLM,CMLM,ECMLM,SUPER
# rel:repetition times
# Authors: You Tang
# Last update: December 31, 2014
##############################################################################################
if(is.null(myG)||is.null(myGD)||is.null(myGM)||is.null(myKI)){stop("Read data Invalid. Please select read valid flies !")}
if(is.null(rel))
rel=100
if(is.null(h2))
h2=0.85
if(is.null(NQTN))
NQTN=5
X<-myGD[,-1]
taxa<-myGD[,1]
taxa<-as.character(taxa)
##simulation phyenotype
##-------------------------##
n=nrow(X)
m=ncol(X)
rep.power.GLM<-data.frame(matrix(0,100,6))
rep.FDR.GLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.GLM<-data.frame(matrix(0,12,6))
rep.power.MLM<-data.frame(matrix(0,100,6))
rep.FDR.MLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.MLM<-data.frame(matrix(0,12,6))
rep.power.SUPER<-data.frame(matrix(0,100,6))
rep.FDR.SUPER<-data.frame(matrix(0,100,6))
rep.Power.Alpha.SUPER<-data.frame(matrix(0,12,6))
rep.power.CMLM<-data.frame(matrix(0,100,6))
rep.FDR.CMLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.CMLM<-data.frame(matrix(0,12,6))
rep.power.ECMLM<-data.frame(matrix(0,100,6))
rep.FDR.ECMLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.ECMLM<-data.frame(matrix(0,12,6))
##PCA
##---------------------##
PCA<-prcomp(X)
PCVar<-PCA$sdev^2
myPC<-PCA$x[,1:3]
m1<-as.data.frame(myPC)
myCV<-cbind(taxa,m1)
myCV<-as.data.frame(myCV)
##-----end step 2 for tfam---###
kcv1<-matrix(1,nrow(myCV),1)
kcv<-cbind(data.frame(kcv1),myCV)
write.table(kcv,"pca.txt",row.names = FALSE,col.names = FALSE,sep="\t",quote=FALSE)
for(i in 1:rel)
{
addm<-matrix(rnorm(NQTN,0,1),NQTN,1)
QTN.position<-sample(1:m,NQTN,replace=FALSE)
SNPQ<-as.matrix(X[,QTN.position])
ge<-SNPQ%*%addm
vg<-var(ge)
ve<-vg*(1-h2)/h2
SDE<-sqrt(ve)
res<-rnorm(n,0,SDE)
y=as.data.frame(ge+res)
myY<-cbind(taxa,y)
myY<-as.data.frame(myY)
max.groups=nrow(myY)
print(paste("*****************","GWAS by GAPIT...GLM model",i," totle:",rel,sep=""))
#--------------------------
myGAPIT_GLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
PCA.total=3,
file.output=FALSE,
model="GLM",
memo="GLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("*****************","GWAS by GAPIT...MLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_MLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
file.output=FALSE,
model="MLM",
memo="MLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("*****************","GWAS by GAPIT...SUPER model",i," totle:",rel,sep=""))
##--------------------------------#
myGAPIT_SUPER <- GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
#PCA.total=3,
model="SUPER",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
file.output=FALSE,
)
print(paste("$$$$$$$$$$$$$$$","GWAS by GAPIT...CMLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_CMLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
file.output=FALSE,
model="CMLM",
memo="CMLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("-------------------","GWAS by GAPIT...ECMLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_ECMLM=GAPIT(
Y=myY,
G=myG,
#GD=myGD,
#GM=myGM,
#KI=myKI,
#CV=myCV,
PCA.total=3,
kinship.cluster=c("average", "complete", "ward"),
kinship.group=c("Mean", "Max"),
file.output=FALSE,
model="ECMLM",
memo="ECMLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
power_ecmlm<-GAPIT.Power(WS=c(1e0,1e3,1e4,1e5,1e6,1e7), alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1), maxOut=100,seqQTN=QTN.position,GM=myGM,GWAS=myGAPIT_ECMLM$GWAS)
#power #FDR #Power.Alpha
rep.power.GLM<-rep.power.GLM+myGAPIT_GLM$Power
rep.FDR.GLM<-rep.FDR.GLM+myGAPIT_GLM$FDR
rep.Power.Alpha.GLM<-rep.Power.Alpha.GLM+myGAPIT_GLM$Power.Alpha
rep.power.MLM<-rep.power.MLM+myGAPIT_MLM$Power
rep.FDR.MLM<-rep.FDR.MLM+myGAPIT_MLM$FDR
rep.Power.Alpha.MLM<-rep.Power.Alpha.MLM+myGAPIT_MLM$Power.Alpha
rep.power.SUPER<-rep.power.SUPER+myGAPIT_SUPER$Power
rep.FDR.SUPER<-rep.FDR.SUPER+myGAPIT_SUPER$FDR
rep.Power.Alpha.SUPER<-rep.Power.Alpha.SUPER+myGAPIT_SUPER$Power.Alpha
rep.power.CMLM<-rep.power.CMLM+myGAPIT_CMLM$Power
rep.FDR.CMLM<-rep.FDR.CMLM+myGAPIT_CMLM$FDR
rep.Power.Alpha.CMLM<-rep.Power.Alpha.CMLM+myGAPIT_CMLM$Power.Alpha
rep.power.ECMLM<-rep.power.ECMLM+power_ecmlm$Power
rep.FDR.ECMLM<-rep.FDR.ECMLM+power_ecmlm$FDR
rep.Power.Alpha.ECMLM<-rep.Power.Alpha.ECMLM+power_ecmlm$Power.Alpha
gc()
}
#mean
rep.power.GLM<-rep.power.GLM/rel
rep.FDR.GLM<-rep.FDR.GLM/rel
rep.Power.Alpha.GLM<-rep.Power.Alpha.GLM/rel
rep.power.MLM<-rep.power.MLM/rel
rep.FDR.MLM<-rep.FDR.MLM/rel
rep.Power.Alpha.MLM<-rep.Power.Alpha.MLM/rel
rep.power.SUPER<-rep.power.SUPER/rel
rep.FDR.SUPER<-rep.FDR.SUPER/rel
rep.Power.Alpha.SUPER<-rep.Power.Alpha.SUPER/rel
rep.power.CMLM<-rep.power.CMLM/rel
rep.FDR.CMLM<-rep.FDR.CMLM/rel
rep.Power.Alpha.CMLM<-rep.Power.Alpha.CMLM/rel
rep.power.ECMLM<-rep.power.ECMLM/rel
rep.FDR.ECMLM<-rep.FDR.ECMLM/rel
rep.Power.Alpha.ECMLM<-rep.Power.Alpha.ECMLM/rel
#ouput files power FDR for GLM,MLM,SUPER
myWS=c(1e0,1e3,1e4,1e5,1e6,1e7)
myalpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)
colnames(rep.FDR.GLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.GLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.GLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.MLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.MLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.MLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.SUPER)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.SUPER)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.SUPER)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.CMLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.CMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.CMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.ECMLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.ECMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.ECMLM)=paste("Power(",myWS,")",sep="")
write.csv(cbind(rep.FDR.GLM,rep.power.GLM),paste(h2,"_",NQTN,".Power.by.FDR.GLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.GLM),paste(h2,"_",NQTN,".Power.by.TypeI.GLM",".csv",sep=""))
write.csv(cbind(rep.FDR.MLM,rep.power.MLM),paste(h2,"_",NQTN,".Power.by.FDR.MLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.MLM),paste(h2,"_",NQTN,".Power.by.TypeI.MLM",".csv",sep=""))
write.csv(cbind(rep.FDR.SUPER,rep.power.SUPER),paste(h2,"_",NQTN,".Power.by.FDR.SUPER",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.SUPER),paste(h2,"_",NQTN,".Power.by.TypeI.SUPER",".csv",sep=""))
write.csv(cbind(rep.FDR.CMLM,rep.power.CMLM),paste(h2,"_",NQTN,".Power.by.FDR.CMLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.CMLM),paste(h2,"_",NQTN,".Power.by.TypeI.CMLM",".csv",sep=""))
write.csv(cbind(rep.FDR.ECMLM,rep.power.ECMLM),paste(h2,"_",NQTN,".Power.by.FDR.ECMLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.ECMLM),paste(h2,"_",NQTN,".Power.by.TypeI.ECMLM",".csv",sep=""))
write.csv(cbind(rep.FDR.GLM[,6],rep.power.GLM[,6],rep.FDR.MLM[,6],rep.power.MLM[,6],rep.FDR.CMLM[,6],rep.power.CMLM[,6],rep.FDR.ECMLM[,6],rep.power.ECMLM[,6],rep.FDR.SUPER[,6],rep.power.SUPER[,6]),paste(h2,"_",NQTN,".Power.by.FDR.GLM.MLM.SUPER",rel,".csv",sep=""))
name.of.trait=noquote(names(myY)[2])
pdf(paste("GAPIT.Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER.", ".pdf", sep = ""), width = 4.5, height = 4.5,pointsize=9)
par(mar = c(5,6,5,3))
#win.graph(width=6, height=4, pointsize=9)
#palette(c("blue","red","green4","brown4","orange",rainbow(5)))
palette(c("green4","red","blue","brown4","orange",rainbow(5)))
plot(rep.FDR.SUPER[,6],rep.power.SUPER[,6],bg="lightgray",xlab="FDR",ylab="Power",ylim=c(0,1),xlim=c(0,1),main="Power against FDR",type="o",pch=20,col=1,cex=1.0,cex.lab=1.3, cex.axis=1, lwd=2,las=1)
lines(rep.power.ECMLM[,6]~rep.FDR.ECMLM[,6], lwd=2,type="o",pch=20,col=2)
lines(rep.power.CMLM[,6]~rep.FDR.CMLM[,6], lwd=2,type="o",pch=20,col=3)
lines(rep.power.MLM[,6]~rep.FDR.MLM[,6], lwd=2,type="o",pch=20,col=4)
lines(rep.power.GLM[,6]~rep.FDR.GLM[,6], lwd=2,type="o",pch=20,col=5)
legend("bottomright",c("SUPER","ECMLM","CMLM","MLM","GLM"), pch = 20, lty =1,col=c(1:5),lwd=2,cex=1.0,bty="n")
#
dev.off()
###add type I error and power###
kkt<-cbind(rep.Power.Alpha.SUPER[,1],rep.Power.Alpha.ECMLM[,1],rep.Power.Alpha.CMLM[,1],rep.Power.Alpha.MLM[,1],rep.Power.Alpha.GLM[,1])
write.csv(cbind(myalpha,rep.Power.Alpha.SUPER[,1],rep.Power.Alpha.ECMLM[,1],rep.Power.Alpha.CMLM[,1],rep.Power.Alpha.MLM[,1],rep.Power.Alpha.GLM[,1]),paste(h2,"_",NQTN,".Type I error.Power.by.FDR.GLM.MLM.SUPER",rel,".csv",sep=""))
myalpha1<-myalpha/10
pdf(paste("GAPIT.Type I error_Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER.", ".pdf", sep = ""), width = 6, height = 4.5,pointsize=9)
par(mar = c(5,6,5,3))
#win.graph(width=6, height=4, pointsize=9)
#palette(c("blue","red","green4","brown4","orange",rainbow(5)))
palette(c("green4","red","blue","brown4","orange",rainbow(5)))
plot(myalpha1,rep.Power.Alpha.SUPER[,1],log="x",bg="lightgray",xlab="Type I error",ylab="Power",main="Power against FDR",type="o",pch=20,col=1,cex=1.0,cex.lab=1.3, cex.axis=1, lwd=2,las=1,ylim=c(min(kkt),max(kkt)))
#plot(myalpha1,rep.Power.Alpha.SUPER[,1],bg="lightgray",xlab="Type I error",ylab="Power",ylim=c(0,1),xlim=c(0,1),main="Power against FDR",type="o",pch=20,col=1,cex=1.0,cex.lab=1.3, cex.axis=1, lwd=2,las=1)
lines(rep.Power.Alpha.ECMLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=2)
lines(rep.Power.Alpha.CMLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=3)
lines(rep.Power.Alpha.MLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=4)
lines(rep.Power.Alpha.GLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=5)
legend("bottomright",c("SUPER","ECMLM","CMLM","MLM","GLM"), pch = 20, lty =1,col=c(1:5),lwd=2,cex=1.0,bty="n")
#
dev.off()
print(paste("GAPIT.Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER.","successfully!" ,sep = ""))
#return(list(inf_Y_all,ref_Y_all))
}#end compare to GLM,MLM,CMLM,ECMLM,SUPER
#=============================================================================================
`GAPIT.Power.compare.plink` <-function(myG=null,myGD=NULL,myGM=NULL,myKI=NULL,myY=NULL,myCV=NULL,rel=NULL,h2=NULL,NQTN=NULL){
# Object: compare to Power against FDR for GLM,MLM,CMLM,ECMLM,SUPER,PLINK
# rel:repetition times
# Authors: You Tang
# Last update: January 23, 2015
##############################################################################################
if(is.null(myG)||is.null(myGD)||is.null(myGM)||is.null(myKI)){stop("Read data Invalid. Please select read valid flies !")}
if(is.null(rel))
rel=100
if(is.null(h2))
h2=0.85
if(is.null(NQTN))
NQTN=5
X<-myGD[,-1]
taxa<-myGD[,1]
taxa<-as.character(taxa)
##simulation phyenotype
##-------------------------##
n=nrow(X)
m=ncol(X)
####handle plink tped output work direct####
G<-myG[-1,]
GD<-t(X)
v3<-matrix(0,nrow(G),1)
kk<-cbind(data.frame(G[,3]),data.frame(G[,1]),data.frame(v3),data.frame(G[,4]),GD)
b1<-nrow(kk)
b2<-ncol(kk)
for(i in 1:b1){
for(j in 5:b2){
##imput number 1
if(kk[i,j]==0)
kk[i,j]=1
}
}
kk4<-cbind(kk[,5],kk[,5])
for(j in 6:b2){
kk4<-cbind(data.frame(kk4),data.frame(kk[,j]),data.frame(kk[,j]))
}
kk6<-cbind(kk[,1:4],kk4)
##output plink deal with tped
write.table(data.frame(kk6),"mdp_numeric.tped",row.names = FALSE,col.names = FALSE,sep="\t",quote=FALSE)
################----------end tped for pinlk-------------##########
rep.power.GLM<-data.frame(matrix(0,100,6))
rep.FDR.GLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.GLM<-data.frame(matrix(0,12,6))
rep.power.MLM<-data.frame(matrix(0,100,6))
rep.FDR.MLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.MLM<-data.frame(matrix(0,12,6))
rep.power.SUPER<-data.frame(matrix(0,100,6))
rep.FDR.SUPER<-data.frame(matrix(0,100,6))
rep.Power.Alpha.SUPER<-data.frame(matrix(0,12,6))
rep.power.CMLM<-data.frame(matrix(0,100,6))
rep.FDR.CMLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.CMLM<-data.frame(matrix(0,12,6))
rep.power.ECMLM<-data.frame(matrix(0,100,6))
rep.FDR.ECMLM<-data.frame(matrix(0,100,6))
rep.Power.Alpha.ECMLM<-data.frame(matrix(0,12,6))
#####------handle tfam for plink----###
rep.power.plink<-data.frame(matrix(0,100,6))
rep.FDR.plink<-data.frame(matrix(0,100,6))
rep.Power.Alpha.plink<-data.frame(matrix(0,12,6))
k1<-matrix(1,n,1)
k2<-matrix(-9,n,2)
##------step 1 end-----------##
WS=c(1e0,1e3,1e4,1e5,1e6,1e7)
alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)
maxOut=100
##PCA
##---------------------##
PCA<-prcomp(X)
PCVar<-PCA$sdev^2
myPC<-PCA$x[,1:3]
m1<-as.data.frame(myPC)
myCV<-cbind(taxa,m1)
myCV<-as.data.frame(myCV)
##-----end step 2 for tfam---###
kcv1<-matrix(1,nrow(myCV),1)
kcv<-cbind(data.frame(kcv1),myCV)
write.table(kcv,"pca.txt",row.names = FALSE,col.names = FALSE,sep="\t",quote=FALSE)
for(i in 1:rel)
{
addm<-matrix(rnorm(NQTN,0,1),NQTN,1)
QTN.position<-sample(1:m,NQTN,replace=FALSE)
SNPQ<-as.matrix(X[,QTN.position])
ge<-SNPQ%*%addm
vg<-var(ge)
ve<-vg*(1-h2)/h2
SDE<-sqrt(ve)
res<-rnorm(n,0,SDE)
y=as.data.frame(ge+res)
myY<-cbind(taxa,y)
myY<-as.data.frame(myY)
##-----output tfam for plink----##
k3<-cbind(data.frame(k1),data.frame(taxa),data.frame(k2),data.frame(k1),data.frame(myY[,2]))
write.table(k3,paste("mdp_numeric",i,".tfam",sep=""),row.names = FALSE,col.names = FALSE,sep="\t",quote=FALSE)
##-----end step 2 for tfam---###
max.groups=nrow(y)
print(paste("*****************","GWAS by GAPIT...GLM model",i," totle:",rel,sep=""))
#--------------------------
myGAPIT_GLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
PCA.total=3,
file.output=FALSE,
group.from=0,
group.to=0,
group.by=0,
memo="GLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("*****************","GWAS by GAPIT...MLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_MLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
file.output=FALSE,
group.from=max.groups,
group.to=max.groups,
group.by=10,
memo="MLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("*****************","GWAS by GAPIT...SUPER model",i," totle:",rel,sep=""))
##--------------------------------#
myGAPIT_SUPER <- GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
#PCA.total=3,
sangwich.top="MLM", #options are GLM,MLM,CMLM, FaST and SUPER
sangwich.bottom="SUPER", #options are GLM,MLM,CMLM, FaST and SUPER
LD=0.1,
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
file.output=FALSE,
)
print(paste("$$$$$$$$$$$$$$$","GWAS by GAPIT...CMLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_CMLM=GAPIT(
Y=myY,
GD=myGD,
GM=myGM,
KI=myKI,
CV=myCV,
file.output=FALSE,
group.from=0,
group.to=max.groups,
group.by=10,
memo="CMLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
print(paste("-------------------","GWAS by GAPIT...ECMLM model",i," totle:",rel,sep=""))
#--------------------------------#
myGAPIT_ECMLM=GAPIT(
Y=myY,
G=myG,
#GD=myGD,
#GM=myGM,
#KI=myKI,
#CV=myCV,
PCA.total=3,
kinship.cluster=c("average", "complete", "ward"),
kinship.group=c("Mean", "Max"),
file.output=FALSE,
group.from=0,
group.to=max.groups,
group.by=10,
memo="ECMLM",
QTN.position=QTN.position,
threshold.output=0.001,
iteration.output=TRUE,
)
##ecmlm power
power_ecmlm<-GAPIT.Power(WS=WS, alpha=alpha, maxOut=maxOut,seqQTN=QTN.position,GM=myGM,GWAS=myGAPIT_ECMLM$GWAS)
##-------------GAWS for plink-----##
##---output gwas.mdp_numericx.qassoc by plink.exe,so must be copy it to work path!----##
system(paste('"plink.exe"', paste('--tped mdp_numeric.tped --tfam mdp_numeric',i,'.tfam --assoc --out gwas.mdp_numeric',i,sep='')), wait = TRUE)
##-------------GAWS for plink-----##
##---output gwas.mdp_numericx.qassoc by plink.exe,so must be copy it to work path!----##
system(paste('"plink.exe"', paste('--tped mdp_numeric.tped --tfam mdp_numeric',i,'.tfam --covar pca.txt --linear --hide-covar --out gwas.mdp_numeric',i,sep='')), wait = TRUE)
plinkGWAS<-read.table(paste("gwas.mdp_numeric",i,".assoc.linear",sep=""),header=T)
Format_GWAS=cbind(myGM,plinkGWAS[,9],rep(NA,nrow(myGM)),rep(NA,nrow(myGM)),rep(NA,nrow(myGM)))
names(Format_GWAS)<-c("SNP","Chromosome","Position","P.value","maf","nobs","FDR_Adjusted_P-values")
power_plink<-GAPIT.Power(WS=WS, alpha=alpha, maxOut=maxOut,seqQTN=QTN.position,GM=myGM,GWAS=Format_GWAS)
##---end powe_plink-----###
##----end step 3 for plink----###
#power #FDR #Power.Alpha
rep.power.GLM<-rep.power.GLM+myGAPIT_GLM$Power
rep.FDR.GLM<-rep.FDR.GLM+myGAPIT_GLM$FDR
rep.Power.Alpha.GLM<-rep.Power.Alpha.GLM+myGAPIT_GLM$Power.Alpha
rep.power.MLM<-rep.power.MLM+myGAPIT_MLM$Power
rep.FDR.MLM<-rep.FDR.MLM+myGAPIT_MLM$FDR
rep.Power.Alpha.MLM<-rep.Power.Alpha.MLM+myGAPIT_MLM$Power.Alpha
rep.power.SUPER<-rep.power.SUPER+myGAPIT_SUPER$Power
rep.FDR.SUPER<-rep.FDR.SUPER+myGAPIT_SUPER$FDR
rep.Power.Alpha.SUPER<-rep.Power.Alpha.SUPER+myGAPIT_SUPER$Power.Alpha
rep.power.CMLM<-rep.power.CMLM+myGAPIT_CMLM$Power
rep.FDR.CMLM<-rep.FDR.CMLM+myGAPIT_CMLM$FDR
rep.Power.Alpha.CMLM<-rep.Power.Alpha.CMLM+myGAPIT_CMLM$Power.Alpha
rep.power.ECMLM<-rep.power.ECMLM+power_ecmlm$Power
rep.FDR.ECMLM<-rep.FDR.ECMLM+power_ecmlm$FDR
rep.Power.Alpha.ECMLM<-rep.Power.Alpha.ECMLM+power_ecmlm$Power.Alpha
##----power-fdr save for mean of plink---##
rep.power.plink<-rep.power.plink+power_plink$Power
rep.FDR.plink<-rep.FDR.plink+power_plink$FDR
rep.Power.Alpha.plink<-rep.Power.Alpha.plink+power_plink$Power.Alpha
##---end sum for power of plink ----##
gc()
}
#mean
rep.power.GLM<-rep.power.GLM/rel
rep.FDR.GLM<-rep.FDR.GLM/rel
rep.Power.Alpha.GLM<-rep.Power.Alpha.GLM/rel
rep.power.MLM<-rep.power.MLM/rel
rep.FDR.MLM<-rep.FDR.MLM/rel
rep.Power.Alpha.MLM<-rep.Power.Alpha.MLM/rel
rep.power.SUPER<-rep.power.SUPER/rel
rep.FDR.SUPER<-rep.FDR.SUPER/rel
rep.Power.Alpha.SUPER<-rep.Power.Alpha.SUPER/rel
rep.power.CMLM<-rep.power.CMLM/rel
rep.FDR.CMLM<-rep.FDR.CMLM/rel
rep.Power.Alpha.CMLM<-rep.Power.Alpha.CMLM/rel
rep.power.ECMLM<-rep.power.ECMLM/rel
rep.FDR.ECMLM<-rep.FDR.ECMLM/rel
rep.Power.Alpha.ECMLM<-rep.Power.Alpha.ECMLM/rel
rep.power.plink<-rep.power.plink/rel
rep.FDR.plink<-rep.FDR.plink/rel
rep.Power.Alpha.plink<-rep.Power.Alpha.plink/rel
#ouput files power FDR for GLM,MLM,SUPER
myWS=c(1e0,1e3,1e4,1e5,1e6,1e7)
myalpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)
colnames(rep.FDR.GLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.GLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.GLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.MLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.MLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.MLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.SUPER)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.SUPER)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.SUPER)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.CMLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.CMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.CMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.ECMLM)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.ECMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.ECMLM)=paste("Power(",myWS,")",sep="")
colnames(rep.FDR.plink)= paste("FDR(",myWS,")",sep="")
colnames(rep.power.plink)=paste("Power(",myWS,")",sep="")
colnames(rep.Power.Alpha.plink)=paste("Power(",myWS,")",sep="")
write.csv(cbind(rep.FDR.GLM,rep.power.GLM),paste(h2,"_",NQTN,".Power.by.FDR.GLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.GLM),paste(h2,"_",NQTN,".Power.by.TypeI.GLM",".csv",sep=""))
write.csv(cbind(rep.FDR.MLM,rep.power.MLM),paste(h2,"_",NQTN,".Power.by.FDR.MLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.MLM),paste(h2,"_",NQTN,".Power.by.TypeI.MLM",".csv",sep=""))
write.csv(cbind(rep.FDR.SUPER,rep.power.SUPER),paste(h2,"_",NQTN,".Power.by.FDR.SUPER",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.SUPER),paste(h2,"_",NQTN,".Power.by.TypeI.SUPER",".csv",sep=""))
write.csv(cbind(rep.FDR.CMLM,rep.power.CMLM),paste(h2,"_",NQTN,".Power.by.FDR.CMLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.CMLM),paste(h2,"_",NQTN,".Power.by.TypeI.CMLM",".csv",sep=""))
write.csv(cbind(rep.FDR.ECMLM,rep.power.ECMLM),paste(h2,"_",NQTN,".Power.by.FDR.ECMLM",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.ECMLM),paste(h2,"_",NQTN,".Power.by.TypeI.ECMLM",".csv",sep=""))
write.csv(cbind(rep.FDR.plink,rep.power.plink),paste(h2,"_",NQTN,".Power.by.FDR.plink",rel,".csv",sep=""))
write.csv(cbind(myalpha,rep.Power.Alpha.plink),paste(h2,"_",NQTN,".Power.by.TypeI.plink",".csv",sep=""))
write.csv(cbind(rep.FDR.GLM[,6],rep.power.GLM[,6],rep.FDR.MLM[,6],rep.power.MLM[,6],rep.FDR.CMLM[,6],rep.power.CMLM[,6],rep.FDR.ECMLM[,6],rep.power.ECMLM[,6],rep.FDR.SUPER[,6],rep.power.SUPER[,6],rep.FDR.plink[,6],rep.power.plink[,6]),paste(h2,"_",NQTN,".Power.by.FDR.GLM.MLM.SUPER.plink",rel,".csv",sep=""))
name.of.trait=noquote(names(myY)[2])
pdf(paste("GAPIT.Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER.plink", ".pdf", sep = ""), width = 4.5, height = 4,pointsize=9)
par(mar = c(5,6,5,3))
#win.graph(width=6, height=4, pointsize=9)
palette(c("green4","red","blue","brown4","orange","black",rainbow(6)))
plot(rep.FDR.SUPER[,6],rep.power.SUPER[,6],bg="lightgray",xlab="FDR",ylab="Power",ylim=c(0,1),xlim=c(0,1),main="Power against FDR",type="o",pch=20,col=1,cex=1.0,cex.lab=1.3, cex.axis=1, lwd=2,las=1)
lines(rep.power.ECMLM[,6]~rep.FDR.ECMLM[,6], lwd=2,type="o",pch=20,col=2)
lines(rep.power.CMLM[,6]~rep.FDR.CMLM[,6], lwd=2,type="o",pch=20,col=3)
lines(rep.power.MLM[,6]~rep.FDR.MLM[,6], lwd=2,type="o",pch=20,col=4)
lines(rep.power.GLM[,6]~rep.FDR.GLM[,6], lwd=2,type="o",pch=20,col=5)
lines(rep.power.plink[,6]~rep.FDR.plink[,6], lwd=2,type="o",pch=20,col=6,lty =1)
legend("bottomright",c("SUPER","ECMLM","CMLM","MLM","GLM","PLINK"), pch =c(20,20,20,20,20,20), lty =c(1,1,1,1,1,2),col=c(1:6),lwd=2,cex=1.0,bty="n")
#
dev.off()
###add type I error and power###
kkt<-cbind(rep.Power.Alpha.SUPER[,1],rep.Power.Alpha.ECMLM[,1],rep.Power.Alpha.CMLM[,1],rep.Power.Alpha.MLM[,1],rep.Power.Alpha.GLM[,1],rep.Power.Alpha.plink[,1])
write.csv(cbind(myalpha,rep.Power.Alpha.SUPER[,1],rep.Power.Alpha.ECMLM[,1],rep.Power.Alpha.CMLM[,1],rep.Power.Alpha.MLM[,1],rep.Power.Alpha.GLM[,1],rep.Power.Alpha.plink[,1]),paste(h2,"_",NQTN,".Type I error.Power.by.FDR.GLM.MLM.SUPER",rel,".csv",sep=""))
myalpha1<-myalpha/10
pdf(paste("GAPIT.Type I error_Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER,plink", ".pdf", sep = ""), width = 6, height = 4.5,pointsize=9)
par(mar = c(5,6,5,3))
palette(c("green4","red","blue","brown4","orange","black",rainbow(6)))
plot(myalpha1,rep.Power.Alpha.SUPER[,1],log="x",bg="lightgray",xlab="Type I error",ylab="Power",main="Power against FDR",type="o",pch=20,col=1,cex=1.0,cex.lab=1.3, cex.axis=1, lwd=2,las=1,ylim=c(min(kkt),max(kkt)))
lines(rep.Power.Alpha.ECMLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=2)
lines(rep.Power.Alpha.CMLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=3)
lines(rep.Power.Alpha.MLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=4)
lines(rep.Power.Alpha.GLM[,1]~myalpha1, lwd=2,type="o",pch=20,col=5)
lines(rep.Power.Alpha.plink[,1]~myalpha1, lwd=2,type="o",pch=20,col=6,lty =1)
legend("bottomright",c("SUPER","ECMLM","CMLM","MLM","GLM","PLINK"), pch =c(20,20,20,20,20,20), lty =c(1,1,1,1,1,2),col=c(1:6),lwd=2,cex=1.0,bty="n")
dev.off()
print(paste("GAPIT.Power ", name.of.trait,".compare to GLM,MLM,CMLM,ECMLM,SUPER,PLINK.","successfully!" ,sep = ""))
#return(list(inf_Y_all,ref_Y_all))
}#end compare to GLM,MLM,SUPER
#=============================================================================================
`GAPIT.Prediction` <-function(myK=NULL,y=NULL, num=NULL){
# Object: Genetic Prediction one time by cross validation and cMLM,result:a pdf of the scree plot
# myK:Kinship
# Y: phenotype with columns of taxa,Y1,Y2...
# num:folders number
# Authors: Jiabo Wang and You Tang
# Last update: December 31, 2014
##############################################################################################
if(is.null(myK)||is.null(y)){stop("Validation Invalid. Please select read valid flies !")}
if(is.null(num))
{
num=5 #not input num value,default folders number is 5
}
y=y[,1:2]
m=nrow(y)
m.sample=round(m/num)
if(num<2||num>m){stop("Validation Invalid. Please select folders num >1 !")}
vali<-matrix(nr=m.sample,nc=num-1)
cali<-matrix(nr=m-m.sample,nc=num-1)
#vali<-list(v1=unique(as.character(sample(y$Taxa, m.sample))))
#cali<-list(c1=y[!(y$Taxa %in% as.matrix(as.data.frame(vali[1]))), 'Taxa'])
vali[,1]<-unique(as.character(sample(y$Taxa, m.sample)))
cali[,1]<-unique(as.character(y[!(y$Taxa %in% vali[,1]), 'Taxa']))
for(j in 2:num)
{
if(j!=num)
{
vali[,j]<-unique(as.character(sample(y[!(y$Taxa %in% vali[,1:j-1]), 'Taxa'], m.sample) ))
}
if(j==num)
{
valilast=unique(as.character(y[!(y$Taxa %in% vali[,1:j-1]), 'Taxa']))
}
if(j!=num)
cali[,j]<-unique(as.character(y[!(y$Taxa %in% vali[,j]), 'Taxa']))
if(j==num)
calilast <<- y[!(y$Taxa %in% valilast), 'Taxa']
}
i=sample(1:num, size = 1)
if(i!=num){
lines.vali<-vali[,i]
}else{
lines.vali<-valilast
}
#use only genotypes that were genotyped and phenotyped
commonGeno_v <- lines.vali[lines.vali %in% myK[,1]]
yvali<- y[match(commonGeno_v,y$Taxa),]
if(i!=num){
lines.cali<-cali[,i]
}else{
lines.cali<-calilast
}
#use only genotypes that were genotyped and phenotyped
commonGeno_c <- lines.cali[lines.cali %in% myK[,1]]
ycali<- y[match(commonGeno_c,y$Taxa),]
Y.raw=ycali[,c(1,2)]#choos a trait
myY=Y.raw
myKI=myK
max.groups=m
#Run GAPIT
#############################################
blupGAPIT <- GAPIT(
Y=myY,
KI=myKI,
#group.from=max.groups,
group.from=1,
group.to=max.groups,
#group.by=10,
#PCA.total=3,
SNP.test=FALSE,
file.output=FALSE
)
blup_prediction=blupGAPIT$GPS
blue<-blupGAPIT$Pred$BLUE
mean_blue<-mean(blue)
blup_prediction.ref<-blup_prediction[match(commonGeno_c,blup_prediction$Taxa),]
blup_prediction.inf<-blup_prediction[match(commonGeno_v,blup_prediction$Taxa),]
inf_BLUP<-blup_prediction.inf$BLUP
ref_BLUP<-blup_prediction.ref$BLUP
inf_pred<-inf_BLUP+mean_blue
ref_pred<-ref_BLUP+mean_blue
inf_all<-cbind(blup_prediction.inf,inf_pred)
ref_all<-cbind(blup_prediction.ref,ref_pred)
inf_Y_all<-merge(y,inf_all,by.x="Taxa",by.y="Taxa")
ref_Y_all<-merge(y,ref_all,by.x="Taxa",by.y="Taxa")
name.of.trait=noquote(names(Y.raw)[2])
pdf(paste("GAPIT.Prediction ", name.of.trait,".Predict reference.pdf", sep = ""), width =6, height = 6)
par(mar = c(5,5,5,5))
plot(ref_Y_all[,2],ref_Y_all[,8],pch=1,xlab="Observed(Ref)",ylab="Predicted(Ref)",cex.lab=1.3,cex.axis=1.2,lwd=2) #xlim=c(50,110),ylim=c(50,110),
kr<-lm(ref_Y_all[,8]~ref_Y_all[,2])
abline(a = kr$coefficients[1], b = kr$coefficients[2], col = "red",lwd=4,lty=1)
#v1<-max(ref_Y_all[,2]])*10/10
#text(v1,kr$coefficients[1]+kr$coefficients[2]*v1,paste("R^2=",format(kr$coefficients[2], digits = 3),seq=""), col = "blue", adj = c(0, -.1))
legend("bottomright",paste("R^2=",format(kr$coefficients[2], digits = 4),seq=""), col="white",text.col="blue",lwd=2,cex=1.2,bty="n")
dev.off()
pdf(paste("GAPIT.Prediction ", name.of.trait,".Predict inference.pdf", sep = ""), width = 6, height = 6)
par(mar = c(5,5,5,5))
plot(inf_Y_all[,2],inf_Y_all[,8],pch=1,xlab="Observed(Inf)",ylab="Predicted(Inf)",cex.lab=1.5,lwd=2,,cex.axis=1.2)#xlim=c(50,110),ylim=c(45,100),
ki<-lm(inf_Y_all[,8]~inf_Y_all[,2])
abline(a = ki$coefficients[1], b = ki$coefficients[2], col = "red",lwd=3,lty=1)
#v0<-max(inf_Y_all[,2])
#text(v0,ki$coefficients[1]+ki$coefficients[2]*v0,paste("R^2=",format(ki$coefficients[2], digits = 4),seq=""), col = "blue", adj = c(0, -.1))
legend("bottomright",paste("R^2=",format(ki$coefficients[2], digits = 4),seq=""), col="white",text.col="blue",lwd=2,cex=1.2,bty="n")
dev.off()
print(paste("GAPIT.Prediction ", name.of.trait,".Predict phenotype.","successfully!" ,sep = ""))
return(list(inf_Y_all,ref_Y_all))
}
#end Prediction one time
#=============================================================================================
`GAPIT.Pruning` <-
function(values,DPP=5000){
#Object: To get index of subset that evenly distribute
#Output: Index
#Authors: Zhiwu Zhang
# Last update: May 28, 2011
##############################################################################################
#No change if below the requirement
if(length(values)<=DPP)return(c(1:length(values)))
#values= log.P.values
values=sqrt(values) #This shift the weight a little bit to the low building.
#Handler of bias plot
rv=runif(length(values))
values=values+rv
values=values[order(values,decreasing = T)]
theMin=min(values)
theMax=max(values)
range=theMax-theMin
interval=range/DPP
ladder=round(values/interval)
ladder2=c(ladder[-1],0)
keep=ladder-ladder2
index=which(keep>0)
return(index)
}#end of GAPIT.Pruning
#=============================================================================================
`GAPIT.QC` <-
function(Y=NULL,KI=NULL,GT=NULL,CV=NULL,Z=NULL,GK=NULL){
#Object: to do data quality control
#Output: Y, KI, GD, CV, Z, flag
#Authors: Zhiwu Zhang and Alex Lipka
# Last update: April 14, 2011
##############################################################################################
#Remove duplicates
print("Removing duplicates...")
#print(dim(CV))
Y=GAPIT.RemoveDuplicate(Y)
CV=GAPIT.RemoveDuplicate(CV)
GK=GAPIT.RemoveDuplicate(GK)
if(!is.null(Z))Z=GAPIT.RemoveDuplicate(Z)
#Remove missing phenotype
print("Removing NaN...")
Y=Y[which(Y[,2]!="NaN"),]
# Remove duplicates for GT
# GT row wise, Z column wise, and KI both direction.
print("Remove duplicates for GT...")
#print(dim(GT))
if(!is.null(GT))
{
if(is.null(dim(GT)))taxa.kept=unique(GT)
if(!is.null(dim(GT)))taxa.kept=unique(GT[,1])
}else{
taxa.kept=unique(Y[,1])
}
# Remove duplicates for KI
print("Remove duplicates for KI...")
# improve speed: remove t() and use cbind
if(!is.null(KI))
{
taxa.all=KI[,1]
taxa.uniqe=unique(taxa.all)
position=match(taxa.uniqe, taxa.all,nomatch = 0)
position.addition=cbind(1,t(1+position))
KI=KI[position,position.addition]
}
#Sort KI
if(!is.null(KI))
{
taxa.all=KI[,1]
position=order(taxa.all)
position.addition=cbind(1,t(1+position))
KI=KI[position,position.addition]
}
# Remove duplicates for Z rowwise
print("Remove duplicates for Z (column wise)...")
if(!is.null(Z))
{
taxa.all=as.matrix(Z[1,])
taxa.uniqe=intersect(taxa.all,taxa.all)
position=match(taxa.uniqe, taxa.all,nomatch = 0)
Z=Z[,position]
}
#Remove the columns of Z if they are not in KI/GT. KI/GT are allowed to have individuals not in Z
print("Maching Z with Kinship colwise...")
if(!is.null(KI))
{
taxa.all=KI[,1]
taxa.kinship=unique(taxa.all)
}
if(!is.null(Z) & !is.null(KI))
{
#get common taxe between KI and Z
taxa.Z=as.matrix(Z[1,])
#taxa.Z=colnames(Z) #This does not work for names starting with numerical or "-" \
if(is.null(KI)){
taxa.Z_K_common=taxa.Z
}else{
taxa.Z_K_common=intersect(taxa.kinship,taxa.Z)
}
Z <-cbind(Z[,1], Z[,match(taxa.Z_K_common, taxa.Z, nomatch = 0)])
#Remove the rows of Z if all the ellements sum to 0
#@@@ improve speed: too many Zs
print("Maching Z without origin...")
Z1=Z[-1,-1]
Z2=data.frame(Z1)
Z3=as.matrix(Z2)
Z4=as.numeric(Z3) #one dimemtion
Z5=matrix(data = Z4, nrow = nrow(Z1), ncol = ncol(Z1))
RS=rowSums(Z5)>0
#The above process could be simplified!
Z <- Z[c(TRUE,RS),]
#make individuals the same in Z, Y, GT and CV
print("Maching GT and CV...")
if(length(Z)<=1)stop("GAPIT says: there is no place to match IDs!")
}# end of if(!is.null(Z) & !is.null(K))
# get intersect of all the data
taxa=intersect(Y[,1],Y[,1])
if(!is.null(Z))taxa=intersect(Z[-1,1],taxa)
if(!is.null(GT))taxa=intersect(taxa,taxa.kept)
if(!is.null(CV))taxa=intersect(taxa,CV[,1])
if(!is.null(GK))taxa=intersect(taxa,GK[,1])
if(length(taxa)<=1)stop("GAPIT says: There is no individual ID matched to covariate. Please check!")
if(!is.null(Z))
{
#Remove taxa in Z that are not in others, columnwise
t=c(TRUE, Z[-1,1]%in%taxa)
if(length(t)<=2)stop("GAPIT says: There is no individual ID matched among data. Please check!")
Z <- Z[t,]
#Remove the columns of Z if all the ellements sum to 0
print("QC final process...")
#@@@ improve speed: too many Zs
Z1=Z[-1,-1]
Z2=data.frame(Z1)
Z3=as.matrix(Z2)
Z4=as.numeric(Z3) #one dimemtion
Z5=matrix(data = Z4, nrow = nrow(Z1), ncol = ncol(Z1))
CS=colSums(Z5)>0
#The above process could be simplified!
Z <- Z[,c(TRUE,CS)]
}
#Filtering with comman taxa
Y <- Y[Y[,1]%in%taxa,]
if(!is.null(CV)) CV=CV[CV[,1]%in%taxa,]
if(!is.null(GK)) GK=GK[GK[,1]%in%taxa,]
if(!is.null(GT)) taxa.kept=data.frame(taxa.kept[taxa.kept%in%taxa])
#Y <- Y[Y[,1]%in%taxa.kept,]
#To sort Y, GT, CV and Z
Y=Y[order(Y[,1]),]
CV=CV[order(CV[,1]),]
if(!is.null(GK))GK=GK[order(GK[,1]),]
if(!is.null(Z))Z=Z[c(1,1+order(Z[-1,1])),]
#get position of taxa.kept in GT
#position=match(taxa.kept[,1], GT[,1],nomatch = 0)
if(is.null(dim(GT)))position=match(taxa.kept, GT,nomatch = 0)
if(!is.null(dim(GT)))position=match(taxa.kept[,1], GT[,1],nomatch = 0)
if(is.null(dim(taxa.kept)))order.taxa.kept=order(taxa.kept)
if(!is.null(dim(taxa.kept)))order.taxa.kept=order(taxa.kept[,1])
GTindex=position[order.taxa.kept]
flag=nrow(Y)==nrow(Z)-1&nrow(Y)==nrow(GT)&nrow(Y)==nrow(CV)
print("GAPIT.QC accomplished successfully!")
#print(dim(Y))
#print(dim(CV))
#print(dim(KI))
return(list(Y = Y, KI = KI, GT = GT, CV = CV, Z = Z, GK = GK, GTindex=GTindex, flag=flag))
}#The function GAPIT.QC ends here
#=============================================================================================
`GAPIT.QQ` <-
function(P.values, plot.type = "log_P_values", name.of.trait = "Trait",DPP=50000,plot.style="rainbow"){
#Object: Make a QQ-Plot of the P-values
#Options for plot.type = "log_P_values" and "P_values"
#Output: A pdf of the QQ-plot
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: May 9, 2011
##############################################################################################
# Sort the data by the raw P-values
#print("Sorting p values")
#print(paste("Number of P values: ",length(P.values)))
#remove NAs and keep the ones between between 0 and 1
P.values=P.values[!is.na(P.values)]
P.values=P.values[P.values>0]
P.values=P.values[P.values<=1]
if(length(P.values[P.values>0])<1) return(NULL)
N=length(P.values)
DPP=round(DPP/4) #Reduce to 1/4 for QQ plot
P.values <- P.values[order(P.values)]
#Set up the p-value quantiles
#print("Setting p_value_quantiles...")
p_value_quantiles <- (1:length(P.values))/(length(P.values)+1)
if(plot.type == "log_P_values")
{
log.P.values <- -log10(P.values)
log.Quantiles <- -log10(p_value_quantiles)
index=GAPIT.Pruning(log.P.values,DPP=DPP)
log.P.values=log.P.values[index ]
log.Quantiles=log.Quantiles[index]
if(plot.style=="FarmCPU"){
pdf(paste("FarmCPU.", name.of.trait,".QQ-Plot.pdf" ,sep = ""),width = 5,height=5)
par(mar = c(5,6,5,3))
}
if(plot.style=="rainbow"){
pdf(paste("GAPIT.", name.of.trait,".QQ-Plot.pdf" ,sep = ""),width = 5,height=5)
par(mar = c(5,6,5,3))
}
#Add conficence interval
N1=length(log.Quantiles)
## create the confidence intervals
c95 <- rep(NA,N1)
c05 <- rep(NA,N1)
for(j in 1:N1){
i=ceiling((10^-log.Quantiles[j])*N)
if(i==0)i=1
c95[j] <- qbeta(0.95,i,N-i+1)
c05[j] <- qbeta(0.05,i,N-i+1)
#print(c(j,i,c95[j],c05[j]))
}
#CI Lines
#plot(log.Quantiles, -log10(c05), xlim = c(0,max(log.Quantiles)), ylim = c(0,max(log.P.values)), type="l",lty=5, axes=FALSE, xlab="", ylab="",col="black")
#par(new=T)
#plot(log.Quantiles, -log10(c95), xlim = c(0,max(log.Quantiles)), ylim = c(0,max(log.P.values)), type="l",lty=5, axes=FALSE, xlab="", ylab="",col="black")
#CI shade
plot(NULL, xlim = c(0,max(log.Quantiles)), ylim = c(0,max(log.P.values)), type="l",lty=5, lwd = 2, axes=FALSE, xlab="", ylab="",col="gray")
index=length(c95):1
polygon(c(log.Quantiles[index],log.Quantiles),c(-log10(c05)[index],-log10(c95)),col='gray',border=NA)
#Diagonal line
abline(a = 0, b = 1, col = "red",lwd=2)
#data
par(new=T)
if(plot.style=="FarmCPU"){
plot(log.Quantiles, log.P.values, cex.axis=1.1, cex.lab=1.3, lty = 1, lwd = 2, col = "Black" ,bty='l', xlab =expression(Expected~~-log[10](italic(p))), ylab = expression(Observed~~-log[10](italic(p))), main = paste(name.of.trait,sep=""),pch=20)
}
if(plot.style=="rainbow"){
plot(log.Quantiles, log.P.values, xlim = c(0,max(log.Quantiles)), ylim = c(0,max(log.P.values)), cex.axis=1.1, cex.lab=1.3, lty = 1, lwd = 2, col = "Blue" ,xlab =expression(Expected~~-log[10](italic(p))),ylab = expression(Observed~~-log[10](italic(p))), main = paste(name.of.trait,sep=""))
}
dev.off()
}
if(plot.type == "P_values")
{
pdf(paste("QQ-Plot_", name.of.trait,".pdf" ,sep = ""))
par(mar = c(5,5,5,5))
qqplot(p_value_quantiles, P.values, xlim = c(0,1),
ylim = c(0,1), type = "l" , xlab = "Uniform[0,1] Theoretical Quantiles",
lty = 1, lwd = 1, ylab = "Quantiles of P-values from GWAS", col = "Blue",
main = paste(name.of.trait,sep=" "))
abline(a = 0, b = 1, col = "red")
dev.off()
}
#print("GAPIT.QQ accomplished successfully!")
}
#=============================================================================================
`GAPIT` <-
function(Y=NULL,G=NULL,GD=NULL,GM=NULL,KI=NULL,Z=NULL,CV=NULL,CV.Inheritance=NULL,GP=NULL,GK=NULL,
group.from=1000000 ,group.to=1000000,group.by=20,DPP=100000,
kinship.cluster="average", kinship.group='Mean',kinship.algorithm="VanRaden",
bin.from=10000,bin.to=10000,bin.by=10000,inclosure.from=10,inclosure.to=10,inclosure.by=10,
SNP.P3D=TRUE,SNP.effect="Add",SNP.impute="Middle",PCA.total=0, SNP.fraction = 1, seed = NULL, BINS = 20,SNP.test=TRUE,
SNP.MAF=0,FDR.Rate = 1, SNP.FDR=1,SNP.permutation=FALSE,SNP.CV=NULL,SNP.robust="GLM",
file.from=1, file.to=1, file.total=NULL, file.fragment = 99999,file.path=NULL,
file.G=NULL, file.Ext.G=NULL,file.GD=NULL, file.GM=NULL, file.Ext.GD=NULL,file.Ext.GM=NULL,
ngrid = 100, llim = -10, ulim = 10, esp = 1e-10,LD.chromosome=NULL,LD.location=NULL,LD.range=NULL,PCA.col=NULL,PCA.3d=FALSE,NJtree.group=NULL,NJtree.type=c("fan","unrooted"),
sangwich.top=NULL,sangwich.bottom=NULL,QC=TRUE,GTindex=NULL,LD=0.1,plot.bin=10^5,
file.output=TRUE,cutOff=0.01, Model.selection = FALSE,output.numerical = FALSE,
output.hapmap = FALSE, Create.indicator = FALSE,Multi_iter=TRUE,windowsize=5e9,
QTN=NULL, QTN.round=1,QTN.limit=0, QTN.update=TRUE, QTN.method="Penalty", Major.allele.zero = FALSE,
method.GLM="FarmCPU.LM",method.sub="reward",method.sub.final="reward",method.bin="static",bin.size=c(1000000),bin.selection=c(10,20,50,100,200,500,1000),
memo=NULL,Prior=NULL,ncpus=1,maxLoop=3,threshold.output=.01,Inter.Plot=FALSE,Inter.type=c("m","q"),
WS=c(1e0,1e3,1e4,1e5,1e6,1e7),alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),maxOut=100,QTN.position=NULL,CG=NULL,
converge=1,iteration.output=FALSE,acceleration=0,iteration.method="accum",PCA.View.output=TRUE,Geno.View.output=TRUE,plot.style="Oceanic",SUPER_GD=NULL,SUPER_GS=FALSE,
h2=NULL,NQTN=NULL,QTNDist="normal",effectunit=1,category=1,r=0.25,cveff=NULL,a2=0,adim=2,Multiple_analysis=FALSE,
model="MLM",Para=NULL
){
#Object: To perform GWAS and GPS (Genomic Prediction/Selection)
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("--------------------- Welcome to GAPIT ----------------------------")
echo=TRUE
GAPIT.Version=GAPIT.0000()
#
if(!is.null(model))if(!match(model,c("MLM","CMLM","SUPER","GLM","FarmCPU","Blink","MLMM","gBLUP","cBLUP","sBLUP"))) stop(paste("PLease choose one model from ","MLM","CMLM","SUPER","GLM","FarmCPU","Blink","gBLUP","cBLUP","sBLUP",sep=""))
#Allow either KI or K, but not both
if(model%in%c("gBLUP","cBLUP","sBLUP"))
{
SNP.test=FALSE
SUPER_GS=TRUE
}
if(!is.null(KI)&is.null(GD)&is.null(G)&is.null(file.G)&is.null(file.GD))SNP.test=FALSE
model_store=model
for(m in 1:length(model_store))
{
model=model_store[m]
if(!is.null(Y))
{
if(group.from<nrow(Y)) model="CMLM"
}
if(group.to!=group.from)model="CMLM"
if(group.to==1&group.from==1)model="GLM"
if(!is.null(sangwich.bottom)&!is.null(sangwich.bottom))model="SUPER"
if(model=="gBLUP") model="MLM"
if(model=="cBLUP") model="CMLM"
if(model=="sBLUP")
{ model="MLM"
if(!is.null(inclosure.from)&is.null(Para$inclosure.from))Para$inclosure.from=inclosure.from
if(is.null(Para$inclosure.from))Para$inclosure.from=10
if(!is.null(inclosure.to)&is.null(Para$inclosure.to))Para$inclosure.to=inclosure.to
if(is.null(Para$inclosure.to))Para$inclosure.to=100
if(!is.null(inclosure.by)&is.null(Para$inclosure.by))Para$inclosure.by=inclosure.by
if(is.null(Para$inclosure.by))Para$inclosure.by=10
if(!is.null(bin.from)&is.null(Para$bin.from))Para$bin.from=bin.from
if(is.null(Para$bin.from))Para$bin.from=10000
if(!is.null(bin.to)&is.null(Para$bin.to))Para$bin.to=bin.to
if(is.null(Para$bin.to))Para$bin.to=10000
if(!is.null(bin.by)&is.null(Para$bin.by))Para$bin.by=bin.by
if(is.null(Para$bin.by))Para$bin.by=10000
if(!is.null(sangwich.top)&is.null(Para$sangwich.top))Para$sangwich.top=sangwich.top
if(is.null(Para$sangwich.top))Para$sangwich.top="MLM"
if(!is.null(sangwich.bottom)&is.null(Para$sangwich.bottom))Para$sangwich.bottom=sangwich.bottom
if(is.null(Para$sangwich.bottom))Para$sangwich.bottom="SUPER"
}
#CMLM
if(model=="GLM")
{
Para$group.from=1
Para$group.to=1
Para$group.by=10
}
if(model=="MLM")
{
Para$group.from=1000000
Para$group.to=1000000
Para$group.by=10
}
if(model=="CMLM")
{
if(is.null(Para$group.from))Para$group.from=group.from
if(is.null(Para$group.to))Para$group.to=group.to
if(is.null(Para$group.by))Para$group.by=group.by
if(Para$group.from==Para$group.to)Para$group.from=10
if(is.null(Para$group.by))Para$group.by=30
}
if(model=="SUPER")
{
if(!is.null(inclosure.from)&is.null(Para$inclosure.from))Para$inclosure.from=inclosure.from
if(is.null(Para$inclosure.from))Para$inclosure.from=10
if(!is.null(inclosure.to)&is.null(Para$inclosure.to))Para$inclosure.to=inclosure.to
if(is.null(Para$inclosure.to))Para$inclosure.to=100
if(!is.null(inclosure.by)&is.null(Para$inclosure.by))Para$inclosure.by=inclosure.by
if(is.null(Para$inclosure.by))Para$inclosure.by=10
if(!is.null(bin.from)&is.null(Para$bin.from))Para$bin.from=bin.from
if(is.null(Para$bin.from))Para$bin.from=10000
if(!is.null(bin.to)&is.null(Para$bin.to))Para$bin.to=bin.to
if(is.null(Para$bin.to))Para$bin.to=10000
if(!is.null(bin.by)&is.null(Para$bin.by))Para$bin.by=bin.by
if(is.null(Para$bin.by))Para$bin.by=10000
if(!is.null(sangwich.top)&is.null(Para$sangwich.top))Para$sangwich.top=sangwich.top
if(is.null(Para$sangwich.top))Para$sangwich.top="MLM"
if(!is.null(sangwich.bottom)&is.null(Para$sangwich.bottom))Para$sangwich.bottom=sangwich.bottom
if(is.null(Para$sangwich.bottom))Para$sangwich.bottom="SUPER"
}
if(model=="FarmCPU")Para$kinship.algorithm="FarmCPU"
if(model=="MLMM")Para$kinship.algorithm="MLMM"
if(model=="Blink")Para$kinship.algorithm="Blink"
if(is.null(Para$memo)|m>1)Para$memo=model
print(Para$memo)
GAPIT_list=list(group.from=group.from ,group.to=group.to,group.by=group.by,DPP=DPP,kinship.cluster=kinship.cluster, kinship.group=kinship.group,kinship.algorithm=kinship.algorithm,
bin.from=bin.from,bin.to=bin.to,bin.by=bin.by,inclosure.from=inclosure.from,inclosure.to=inclosure.to,inclosure.by=inclosure.by,SNP.P3D=SNP.P3D,SNP.effect=SNP.effect,SNP.impute=SNP.impute,PCA.total=PCA.total, SNP.fraction = SNP.fraction, seed = seed, BINS = 20,SNP.test=SNP.test,
SNP.MAF=SNP.MAF,FDR.Rate = FDR.Rate, SNP.FDR=SNP.FDR,SNP.permutation=SNP.permutation,SNP.CV=NULL,SNP.robust="GLM",file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment,file.path=file.path,
file.G=file.G, file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,ngrid = 100, llim = -10, ulim = 10, esp = 1e-10,Inter.Plot=Inter.Plot,Inter.type=Inter.type,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,PCA.col=PCA.col,PCA.3d=PCA.3d,NJtree.group=NJtree.group,NJtree.type=NJtree.type,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,QC=QC,GTindex=GTindex,LD=LD,plot.bin=plot.bin,file.output=file.output,cutOff=cutOff, Model.selection = Model.selection,output.numerical = output.numerical,
output.hapmap = output.hapmap, Create.indicator = Create.indicator,QTN=QTN, QTN.round=1,QTN.limit=0, QTN.update=TRUE, QTN.method="Penalty", Major.allele.zero = Major.allele.zero,
method.GLM=method.GLM,method.sub=method.sub,method.sub.final="reward",method.bin="static",bin.size=bin.size,bin.selection=bin.selection,model=model,
h2=h2,NQTN=NQTN,QTNDist="normal",effectunit=effectunit,category=category,r=r,cveff=NULL,a2=0,adim=2,Multi_iter=Multi_iter,windowsize=5e9,
memo="",Prior=NULL,ncpus=1,maxLoop=maxLoop,threshold.output=threshold.output,WS=c(1e0,1e3,1e4,1e5,1e6,1e7),alpha=alpha,maxOut=100,QTN.position=QTN.position,CG=CG,
converge=converge,iteration.output=iteration.output,acceleration=0,iteration.method="accum",PCA.View.output=PCA.View.output,Geno.View.output=Geno.View.output,plot.style="Oceanic",SUPER_GD=NULL,SUPER_GS=SUPER_GS,Multiple_analysis=Multiple_analysis)
G_list_M=rownames(as.matrix(GAPIT_list))
P_list_M=rownames(as.matrix(Para))
Para=c(GAPIT_list[!G_list_M%in%P_list_M],Para)
#print(Para$kinship.algorithm)
if(SUPER_GS==TRUE)Para$SNP.test=FALSE
IC=NULL
#GAPIT.Version=GAPIT.0000()
print("--------------------Processing traits----------------------------------")
if(!is.null(Y)){
print("Phenotype provided!")
if(ncol(Y)<2) stop ("Phenotype should have taxa name and one trait at least. Please correct phenotype file!")
if(m==1)
{
DP=GAPIT.DP(G=G,GD=GD,GM=GM,KI=KI,Z=Z,CV=CV,CV.Inheritance=Para$CV.Inheritance,GP=GP,GK=GK,
group.from=Para$group.from ,group.to= Para$group.to,group.by=Para$group.by,DPP= Para$DPP,
kinship.cluster=Para$kinship.cluster, kinship.group=Para$kinship.group,kinship.algorithm=Para$ kinship.algorithm, NJtree.group=Para$NJtree.group,NJtree.type=Para$NJtree.type,plot.bin=Para$plot.bin,PCA.col=Para$PCA.col,PCA.3d=Para$PCA.3d,
sangwich.top=Para$sangwich.top,sangwich.bottom=Para$sangwich.bottom,LD=Para$LD,bin.from= Para$bin.from,bin.to= Para$bin.to,bin.by= Para$bin.by,inclosure.from= Para$inclosure.from,inclosure.to= Para$inclosure.to,inclosure.by= Para$inclosure.by,
SNP.P3D= Para$SNP.P3D,SNP.effect= Para$SNP.effect,SNP.impute= Para$SNP.impute,PCA.total= Para$PCA.total, SNP.fraction = Para$SNP.fraction, seed = Para$seed,
BINS = Para$BINS,SNP.test=Para$SNP.test, SNP.MAF= Para$SNP.MAF,FDR.Rate = Para$FDR.Rate, SNP.FDR= Para$SNP.FDR,SNP.permutation= Para$SNP.permutation,
SNP.CV= Para$SNP.CV,SNP.robust= Para$SNP.robust, Inter.Plot=Para$Inter.Plot, Inter.type=Para$Inter.type,
file.from= Para$file.from, file.to=Para$file.to, file.total= Para$file.total, file.fragment = Para$file.fragment,file.path= Para$file.path,
file.G= Para$file.G, file.Ext.G= Para$file.Ext.G,file.GD= Para$file.GD, file.GM= Para$file.GM, file.Ext.GD= Para$file.Ext.GD,file.Ext.GM= Para$file.Ext.GM,
ngrid = Para$ngrid, llim = Para$llim, ulim = Para$ulim, esp = Para$esp,Multi_iter=Para$Multi_iter,windowsize=Para$windowsize,
LD.chromosome= Para$LD.chromosome,LD.location= Para$LD.location,LD.range= Para$LD.range,
QC= Para$QC,GTindex= Para$GTindex,cutOff=Para$cutOff, Model.selection = Para$Model.selection,output.numerical = Para$output.numerical,
Create.indicator = Para$Create.indicator,QTN= Para$QTN, QTN.round= Para$QTN.round,QTN.limit= Para$QTN.limit, QTN.update= Para$QTN.update, QTN.method= Para$QTN.method, Major.allele.zero = Para$Major.allele.zero,
method.GLM=Para$ method.GLM,method.sub= Para$method.sub,method.sub.final= Para$method.sub.final,
method.bin= Para$method.bin,bin.size= Para$bin.size,bin.selection= Para$bin.selection,
memo= Para$memo,Prior= Para$Prior,ncpus=Para$ncpus,maxLoop= Para$maxLoop,threshold.output= Para$threshold.output,
WS= Para$WS,alpha= Para$alpha,maxOut= Para$maxOut,QTN.position= Para$QTN.position, converge=Para$converge,iteration.output= Para$iteration.output,acceleration=Para$acceleration,
iteration.method= Para$iteration.method,PCA.View.output=Para$PCA.View.output,
output.hapmap = Para$output.hapmap, file.output= Para$file.output,Geno.View.output=Para$Geno.View.output,plot.style=Para$plot.style,SUPER_GD= Para$SUPER_GD,SUPER_GS= Para$SUPER_GS,CG=Para$CG,model=model)
}else{
DP$kinship.algorithm=Para$ kinship.algorithm
DP$group.from=Para$group.from
DP$group.to=Para$group.to
DP$group.by=Para$group.by
DP$sangwich.top=Para$sangwich.top
DP$sangwich.bottom=Para$sangwich.bottom
DP$bin.from= Para$bin.from
DP$bin.to= Para$bin.to
DP$bin.by= Para$bin.by
DP$inclosure.from= Para$inclosure.from
DP$inclosure.to= Para$inclosure.toDP$inclosure.by= Para$inclosure.by
}
for (trait in 2: ncol(Y))
{
traitname=colnames(Y)[trait]
###Statistical distributions of phenotype
###Correlation between phenotype and principal components
print(paste("Processing trait: ",traitname,sep=""))
if(!is.null(Para$memo)) traitname=paste(Para$memo,".",traitname,sep="")
if(!is.null(Y) & Para$file.output)ViewPhenotype<-GAPIT.Phenotype.View(myY=Y[,c(1,trait)],traitname=traitname,memo=Para$memo)
Judge=GAPIT.Judge(Y=Y[,c(1,trait)],G=DP$G,GD=DP$GD,KI=DP$KI,GM=DP$GM,group.to=DP$group.to,group.from=DP$group.from,sangwich.top=DP$sangwich.top,sangwich.bottom=DP$sangwich.bottom,kinship.algorithm=DP$kinship.algorithm,PCA.total=DP$PCA.total,model=DP$model,SNP.test=DP$SNP.test)
DP$group.from=Judge$group.from
DP$group.to=Judge$group.to
DP$name.of.trait=traitname
DP$Y=Y[,c(1,trait)]
DP$model=model
print(Para$SNP.test)
IC=GAPIT.IC(DP=DP)
SS=GAPIT.SS(DP=DP,IC=IC)
if(Para$SNP.test==TRUE)ID=GAPIT.ID(DP=DP,IC=IC,SS=SS)
}#for loop trait
#print(SNP.test)
print("GAPIT accomplished successfully for multiple traits. Result are saved")
print("It is OK to see this: 'There were 50 or more warnings (use warnings() to see the first 50)'")
out <- list()
out$QTN<-QTN.position
out$GWAS<-SS$GWAS
out$Pred<-SS$Pred
out$QTN<-IC$QTN
out$Power<-SS$Power
out$FDR<-SS$FDR
out$Power.Alpha<-SS$Power.Alpha
out$alpha<-SS$alpha
out$mc=SS$mc
out$bc=SS$bc
out$mp=SS$mp
out$h2=SS$h2
out$PCA=IC$PCA
out$GD=DP$GD
out$GM=DP$GM
out$KI=IC$K
out$GM=DP$GM
if(Para$SNP.test==TRUE)names(out$GWAS$P.value)="mp"
if(kinship.algorithm=="FarmCPU")names(out$Pred)=c("Taxa",traitname,"Prediction")
#return (out)
}else{# is.null(Y)
#print(Para$SNP.MAF)
out <- list()
# if(is.null(Para$NQTN)&is.null(Para$h2))
# {
# Para$kinship.algorithm="SUPER"
# Para$PCA.total=0
# }
#print(Para$kinship.algorithm)
#print(Para$PCA.total)
myGenotype<-GAPIT.Genotype(G=G,GD=GD,GM=GM,KI=KI,kinship.algorithm=Para$kinship.algorithm,PCA.total=Para$PCA.total,SNP.fraction=Para$SNP.fraction,SNP.test=Para$SNP.test,
file.path=Para$file.path,file.from=Para$file.from, file.to=Para$file.to, file.total=Para$file.total, file.fragment = Para$file.fragment, file.G=Para$file.G,
file.Ext.G=Para$file.Ext.G,file.GD=Para$file.GD, file.GM=Para$file.GM, file.Ext.GD=Para$file.Ext.GD,file.Ext.GM=Para$file.Ext.GM,
SNP.MAF=Para$SNP.MAF,FDR.Rate = Para$FDR.Rate,SNP.FDR=Para$SNP.FDR,SNP.effect=Para$SNP.effect,SNP.impute=Para$SNP.impute,NJtree.group=Para$NJtree.group,NJtree.type=Para$NJtree.type,
LD.chromosome=Para$LD.chromosome,LD.location=Para$LD.location,LD.range=Para$LD.range,GP=Para$GP,GK=Para$GK,bin.size=NULL,inclosure.size=NULL,
sangwich.top=NULL,sangwich.bottom=Para$sangwich.bottom,GTindex=NULL,file.output=Para$file.output, Create.indicator = Para$Create.indicator, Major.allele.zero = Para$Major.allele.zero,Geno.View.output=Para$Geno.View.output,PCA.col=Para$PCA.col,PCA.3d=Para$PCA.3d)
GD=myGenotype$GD
GI=myGenotype$GI
GT=myGenotype$GT
#G=myGenotype$G
chor_taxa=myGenotype$chor_taxa
rownames(GD)=GT
colnames(GD)=GI[,1]
taxa=GT
#print(GD[1:5,1:5])
if(Para$output.numerical)
{
write.table(cbind(taxa,GD), "GAPIT.Genotype.Numerical.txt", quote = FALSE, sep = "\t", row.names = F,col.names = T)
write.table(GI, "GAPIT.Genotype.map.txt", quote = FALSE, sep = "\t", row.names = F,col.names = T)
}
if(Para$output.hapmap) write.table(myGenotype$G, "GAPIT.Genotype.hmp.txt", quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
#GD=cbind(as.data.frame(GT),GD)
if(!is.null(seed))set.seed(seed)
#print(Para$NQTN)
if(!is.null(Para$NQTN)&!is.null(Para$h2))
{
myG_simulation<-GAPIT.Phenotype.Simulation(GD=cbind(as.data.frame(myGenotype$GT),myGenotype$GD),GM=myGenotype$GI,h2=Para$h2,NQTN=Para$NQTN,QTNDist=Para$QTNDist,effectunit=Para$effectunit,category=Para$category,r=Para$r,cveff=Para$cveff,a2=Para$a2,adim=Para$adim)
out=c(out,myG_simulation)
}
out$GD=data.frame(cbind(as.data.frame(GT),as.data.frame(GD)))
out$GM=GI
out$G=myGenotype$G
out$kinship=myGenotype$KI
out$PCA=myGenotype$PC
}# is.null(Y)
}#end of model loop
#print(tail(IC$GM))
if(!is.null(Y)&SNP.test)if(Multiple_analysis&Para$file.output&length(model_store)*(ncol(Y)-1)>1&length(model_store)*(ncol(Y)-1)<9)
{
#print(DP$QTN.position)
GMM=GAPIT.Multiple.Manhattan(model_store=model_store,Y=Y,GM=IC$GM,seqQTN=DP$QTN.position)
#print(str(GMM$multip_mapP))
GAPIT.Circle.Manhatton.Plot(band=1,r=3,GMM$multip_mapP,plot.type=c("c","q"),signal.line=1,xz=GMM$xz)
}# end of mutiple manhantton plot
# if(!is.null(Y)&!SNP.test&Multiple_analysis&Para$file.output&length(model_store)*(ncol(Y)-1)>1)
# {
# GAPIT.Interactive.GS(model_store=model_store,Y=Y)
# }
return (out)
} #end of GAPIT function
`GAPIT.ROC` <-
function(t=NULL,se=NULL,Vp=1,trait="",plot.style="rainbow"){
#Object: To make table and plot for ROC (power vs FDR)
#Input: t and se are the vectors of t value and their standard error
#Input: Vp is phenotypic variance and trait is name of the phenotype
#Output: A table and plot
#Requirment: error df is same for all SMP or large
#Authors: Zhiwu Zhang
# Last update: Feb 11, 2013
##############################################################################################
#print("GAPIT.ROC start")
#print("Length of t se and Vp")
#print(length(t))
#print(length(se))
#print((Vp))
if(length(t)==length(t[is.na(t)]) ){
#print("NA t, No ROC plot")
return(NULL)
}
#test
#n=1000
#trait="test"
#t=rnorm(n)
#se=sqrt(abs(rnorm(n)) )
#Vp=10
#Remove NAs
index=is.na(t)
t=t[!index]
se=se[!index]
#print(head(cbind(t,se)))
#Configration
FDR=c(0,.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1)
coefficient=c(0,0.01,.02,.05,.1,.2,.3)
#Power holder
nf=length(FDR)
nc=length(coefficient)
power=matrix(NA,nf,nc)
#Handler of matrix format
if(!is.null(dim(t))) t=t[,1]
if(!is.null(dim(se))) se=se[,1]
n=length(t)
#Discard negative
t=abs(t)
#print("@@@@@@@@@@@@@@")
#sort t and se
position=order(t,decreasing = TRUE)
t=t[position]
se=se[position]
EFFECT=coefficient*sqrt(Vp)
newbit=matrix(1/se,n,1)%*%EFFECT #n by nc matrix
tnew=newbit+t #n by nc matrix
for (i in 1:nf){
fdr=FDR[i]
cutpoint=floor(n*fdr)
cutoff=t[cutpoint]
for (j in 1:nc){
effect= EFFECT[j]
singnificant=tnew[,j]>cutoff
count=length(t[singnificant])
power[i,j]=count/n
} #end of for on fdr
} #end of for on effect
#output
rownames(power)=FDR
tkk<-c(.3,.2,.1,.05,.02,0.01,0)
tc1<-c(0,0.25,0.5,0.75,1.0)
#colnames(power)=paste("QTN=",coefficient,sep="")
colnames(power)=paste("QTN=",tkk,sep="")
if(plot.style=="FarmCPU"){
write.table(power,file=paste("FarmCPU.",trait,".ROC.csv",sep=""),quote = TRUE, sep = ",", row.names = TRUE,col.names = NA)
}
if(plot.style=="rainbow"){
write.table(power,file=paste("GAPIT.",trait,".ROC.csv",sep=""),quote = TRUE, sep = ",", row.names = TRUE,col.names = NA)
}
FDR_log<-FDR/10
#palette(c("black","red","blue","brown", "orange","cyan", "green",rainbow(nc)))
if(plot.style=="FarmCPU"){
pdf(paste("FarmCPU.", trait,".ROC.pdf" ,sep = ""), width = 5,height=5)
par(mar = c(5,6,5,3))
}
if(plot.style=="rainbow"){
pdf(paste("GAPIT.", trait,".ROC.pdf" ,sep = ""), width = 7,height=7)
par(mar = c(5,5,5,3))
}
palette(c("black","red","blue","brown", "orange","cyan", "green",rainbow(nc)))
plot(FDR_log,power[,1],log="x",type="o",yaxt="n",lwd=3,col=1,xlab="Type I error",ylab="Power",main = trait,cex.axis=1.3, cex.lab=1.3)
axis(side=2,at=tc1,labels=tc1,cex.lab=1.3,cex.axis=1.3)
for(i in 2:nc){
lines(power[,i]~FDR_log, lwd=3,type="o",pch=i,col=i)
}
#legend("bottomright", colnames(power), pch = c(1:nc), lty = c(1,2),col=c(1:nc))
legend("bottomright", colnames(power), pch = c(nc:1), lty = c(1,2),col=c(nc:1),lwd=2,bty="n")
palette("default") # reset back to the default
#print("@@@@@@@@@@@@@@")
#print(power)
dev.off()
print("ROC completed!")
} #GAPIT.ROC ends here
#=============================================================================================
`GAPIT.RandomModel` <-
function(GWAS,Y,CV=NULL,X,cutOff=0.01,GT=NULL,n_ran=30){
#Object: To calculate the genetics variance ratio of Candidate Genes
#Output: The genetics variance raito between CG and total
#Authors: Jiabo Wang and Zhiwu Zhang
# Last update: Nov 6, 2019
##############################################################################################
if(!require(lme4)) install.packages("lme4")
library("lme4")
#GWAS=myGAPIT_GLM$GWAS
#CV=myGAPIT_GLM$PCA
#cut.set=0.01
print("GAPIT.RandomModel beginning...")
if(is.null(GT))GT=as.character(Y[,1])
name.of.trait=colnames(Y)[2]
cutoff=cutOff/nrow(GWAS)
P.value=as.numeric(GWAS[,4])
P.value[is.na(P.value)]=1
index=P.value<cutoff
#index[c(1:2)]=TRUE
geneGD=X[,index]
geneGWAS=GWAS[index,]
# print(dim(Y))
# print(dim(CV))
# print(dim(geneGD))
if(length(unique(index))==1)
{
print("There is no significant marker for VE !!")
return(list(GVs=NULL))
}
index_T=as.matrix(table(index))
in_True=index_T[rownames(index_T)=="TRUE"]
if(in_True!=1)
{
colnames(geneGD)=paste("gene_",1:in_True,sep="")
}
colnames(Y)=c("taxa","trait")
if(is.null(CV))
{
#CV=cbind(GT,1)
taxa_Y=as.character(Y[,1])
geneGD=geneGD[GT%in%taxa_Y,]
# if(!is.null(PC))PC=PC[taxa_GD%in%taxa_Y,]
Y=Y[taxa_Y%in%GT,]
tree2=cbind(Y,geneGD)
# CV[,2]=1
}else{
if(ncol(CV)==1)
{
taxa_Y=as.character(Y[,1])
geneGD=geneGD[GT%in%taxa_Y,]
# if(!is.null(PC))PC=PC[taxa_GD%in%taxa_Y,]
Y=Y[taxa_Y%in%GT,]
tree2=cbind(Y,geneGD)
}else{
colnames(CV)=c("Taxa",paste("CV",1:(ncol(CV)-1),sep=""))
tree2=cbind(Y,CV[,-1],geneGD)
}
}
if(in_True==1)colnames(tree2)[ncol(tree2)]=paste("gene_",1,sep="")
# print(head(tree2))
# print(dim(CV))
# print(dim(geneGD))
n_cv=ncol(CV)-1
# print(n_cv)
n_gd=in_True
n_id=nrow(Y)
print(n_gd)
print(n_cv)
print(n_id)
if((n_gd+n_cv)>n_ran)
{
print("The candidate markers are more than threshold value !")
return(list(GVs=NULL))
}
if(!is.null(CV))
{
#ff <- paste("trait~1+PC1+PC2+PC3+(1|gene_1)+(1|gene_2)+(1|gene_3)+(1|gene_4)+(1|gene_5)+(1|gene_6)"
#dflme <- lmer(ff, data=tree2)
if(ncol(CV)==1)
{
command0=paste("trait~1",sep="")
command1=command0
command2=command1
for(j in 1:n_gd)
{
command2=paste(command2,"+(1|gene_",j,")",sep="")
}
}else{
command0=paste("trait~1",sep="")
command1=command0
for(i in 1:n_cv)
{
command1=paste(command1,"+CV",i,sep="")
}
command2=command1
for(j in 1:n_gd)
{
command2=paste(command2,"+(1|gene_",j,")",sep="")
}
}
}else{
command0=paste("trait~1",sep="")
command1=command0
command2=command1
for(j in 1:n_gd)
{
command2=paste(command2,"+(1|gene_",j,")",sep="")
}
}
#command3=paste(command2,"+(1|gene_",j,")",sep="")
dflme <- lmer(command2, data=tree2,control=lmerControl(check.nobs.vs.nlev = "ignore",
check.nobs.vs.rankZ = "ignore",
check.nobs.vs.nRE="ignore"))
carcor_matrix=as.data.frame(summary(dflme)$varcor)
var_gene=as.numeric(carcor_matrix[1:(nrow(carcor_matrix)-1),4])
var_res=carcor_matrix[nrow(carcor_matrix),4]
print(paste("Candidate Genes could explain genetics variance :",sep=""))
print(var_gene/sum(var_gene+var_res))
v_rat=var_gene/sum(var_gene+var_res)
gene_list=cbind(geneGWAS,v_rat)
colnames(gene_list)[ncol(gene_list)]="Variance_Explained"
write.csv(gene_list,paste("GAPIT.", name.of.trait,".Phenotype_Variance_Explained_by_Association_Markers.csv",sep=""),quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#gene_list=read.csv("GAPIT.Weight.GrowthIntercept.Phenotype_Variance_Explained_by_Association_Markers.csv",head=T)
if(!is.na(sum(gene_list[1,c(4:8)])))
{
pdf(paste("GAPIT.", name.of.trait,".Effect_VP.pdf" ,sep = ""), width = 7,height=5.75)
par(mar=c(4,5,4,4),cex=0.8)
gene_list=gene_list[order(gene_list$effect),]
plot(gene_list$effect,gene_list$Variance_Explained,
xlab="Estimated Effect",
ylab="Variance Explained of Phenotype"
)
dev.off()
pdf(paste("GAPIT.", name.of.trait,".MAF_VP.pdf" ,sep = ""), width = 7,height=5.75)
par(mar=c(4,5,4,4),cex=0.8)
gene_list=gene_list[order(gene_list$maf),]
plot(gene_list$maf,gene_list$Variance_Explained,xlab="MAF",ylab="Variance Explained of Phenotype")
dev.off()
if(n_gd>=10)
{
pdf(paste("GAPIT.", name.of.trait,".MAF_Effect_VP.pdf" ,sep = ""), width = 9,height=5.75)
n=10
layout(matrix(c(1,1,2,1,1,1,1,1,1),3,3,byrow=TRUE), c(2,1), c(1,1), TRUE)
do_color=colorRampPalette(c("green", "red"))(n)
par(mar=c(4,5,2,8),cex=0.8)
y=gene_list$maf
x=gene_list$effect
x.lim=max(x)+max(x)/10
y.lim=max(y)+max(y)/10
z=gene_list$Variance_Explained
quantile_cut=quantile(z)
r2_color=rep("black",n_gd)
for(i in 1:(n/2))
{
r2_color[z<=quantile_cut[i+1]&z>=quantile_cut[i]]=do_color[2*i]
}
plot(y~x,type="p", ylim=c(0,y.lim), xlim = c(min(x), max(x)),col = r2_color, xlab = "",ylab = "", cex.lab=1.2,pch=21,bg=r2_color)
mtext("Estimated Effect",side=1,line=2.5)
mtext("MAF",side=2,line=2.5)
par(mar=c(2,13,5,4),cex=0.5)
barplot(matrix(rep(0.4,times=n),n,1),beside=T,col=do_color,border=do_color,axes=FALSE,horiz =T)
#legend(x=10,y=2,legend=expression(R^"2"),,lty=0,cex=1.3,bty="n",bg=par("bg"))
step=length(seq(0,round(max(z),3),by=0.01))
small_bar=round(seq(0,round(max(z),3),by=(max(z)-min(z))/10),2)
#main()
mtext("Variance Explained",side=2,line=0.4,col="black",cex=0.5)
axis(4,c(1,6,11),c(min(small_bar),median(small_bar),max(small_bar)),las=2,cex.axis = 0.9,tick=F,line=0)
dev.off()
}
}
return(list(GVs=var_gene/sum(var_gene+var_res)))
}#end of GAPIT.RandomModel function
#=============================================================================================
`GAPIT.RemoveDuplicate` <-
function(Y){
#Object: NA
#Output: NA
#Authors: Zhiwu Zhang
# Last update: Augus 30, 2011
##############################################################################################
return (Y[match(unique(Y[,1]), Y[,1], nomatch = 0), ] )
}
#=============================================================================================
`GAPIT.Report` <-
function(name.of.trait=NULL,GWAS=NULL,pred=pred,ypred=NULL,tvalue=NULL,stderr=NULL,Vp=1,
DPP=100000,cutOff=.01,threshold.output=.01,MAF=NULL,seqQTN=NULL,MAF.calculate=FALSE,plot.style="rainbow"){
#Object: Out put plots and tables
#Input: GWAS,name.of.trait, DPP
#Requirement: None
#Output: Graphs and tables
#Output: return ycor if ypred is not null
#Authors: Zhiwu Zhang
# Date start: April 2, 2013
# Last update: April 2, 2013
##############################################################################################
#print("GAPIT.Report Started")
#print(seqQTN)
#Manhattan Plots
#print("Manhattan plot (Genomewise)..." )
if(plot.style=="FarmCPU"){
GAPIT.Manhattan(GI.MP = GWAS[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff,seqQTN=seqQTN,plot.style=plot.style)
}
if(plot.style=="rainbow"){
GAPIT.Manhattan(GI.MP = GWAS[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Genomewise",cutOff=cutOff,seqQTN=seqQTN,plot.style=plot.style)
#}
#print("Manhattan plot (Chromosomewise)..." )
GAPIT.Manhattan(GI.MP = GWAS[,2:4], name.of.trait = name.of.trait, DPP=DPP, plot.type = "Chromosomewise",cutOff=cutOff,plot.style=plot.style)
}
#QQ plots
#print("QQ plotting..." )
#if(plot.style=="rainbow"){
# GAPIT.QQ(P.values = GWAS[,4], name.of.trait = name.of.trait,DPP=DPP)
#}
#if(plot.style=="nature"){
GAPIT.QQ(P.values = GWAS[,4], name.of.trait = name.of.trait,DPP=DPP,plot.style=plot.style)
#}
#Association Table
#print("Create association table..." )
index=1:nrow(GWAS)
if(threshold.output<1)index=which(GWAS[,4]<threshold.output)
if(plot.style=="FarmCPU"){
write.table(GWAS[index,], paste("FarmCPU.", name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}
if(plot.style=="rainbow"){
write.table(GWAS[index,], paste("GAPIT.", name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}
#Prediction
#print("Create prediction table..." )
#if(!is.null(pred)) write.table(pred, paste("GAPIT.", name.of.trait, ".Pred.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#print("Create prediction table for unknown phenotype...")
#if(!is.null(ypred)) write.table(ypred, paste("GAPIT.", name.of.trait, ".unknownY.Pred.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
if(!is.null(pred) || !is.null(ypred)){
myPred=FarmCPU.Pred(pred=pred,ypred=ypred,name.of.trait=name.of.trait)
}
#ROC
#print("Creating ROC table and plot" )
myROC=GAPIT.ROC(t=tvalue,se=stderr,Vp=Vp,trait=name.of.trait,plot.style=plot.style)
#MAF
#print("Creating MAF table and plot" )
if(MAF.calculate){
myMAF=GAPIT.MAF(MAF=MAF,P=GWAS[,4],E=NULL,trait=name.of.trait,threshold.output=threshold.output,plot.style=plot.style)}
#print("Report accomplished" )
}#The function GAPIT.Report ends here
#=============================================================================================
`GAPIT.SS` <-
function(DP=NULL,IC=NULL){
#Object: To Sufficient Statistics (SS) for GWAS and GS
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novenber 3, 2016
##############################################################################################
print("GAPIT.SS in process...")
#Define the funcitno here
Timmer=GAPIT.Timmer(Infor="GAPIT.SS")
Memory=GAPIT.Memory(Infor="GAPIT.SS")
if(DP$SNP.test)
{
ic_GD=IC$GD
ic_GM=IC$GM
ic_Y=IC$Y
ic_KI=IC$K
ic_PCA=IC$PCA
Z=DP$Z
taxa_Y=as.character(ic_Y[,1])
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GAPIT.QC")
Memory=GAPIT.Memory(Memory=Memory,Infor="GAPIT.QC")
if(DP$kinship.algorithm!="None" & DP$kinship.algorithm!="SUPER" & is.null(Z))
{
Z=as.data.frame(diag(1,nrow(ic_Y)))
Z=rbind(taxa_Y,Z)
taxa=c('Taxa',as.character(taxa_Y))
Z=cbind(taxa,Z)
}
# print(head(ic_PCA))
# print(dim(DP$CV))
# print(head(DP$PC))
if(max(ic_PCA[,2])==min(ic_PCA[,2]))ic_PCA=NULL
#print(head(ic_PCA))
#print("@@@@@")
if (DP$SNP.test&DP$kinship.algorithm%in%c("FarmCPU","Blink","MLMM"))
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GAPIT.FarmCPU")
Memory=GAPIT.Memory(Memory=Memory,Infor="GAPIT.FarmCPU")
myBus=GAPIT.Bus(Y=ic_Y,CV=ic_PCA,Z=NULL,GK=NULL,KI=ic_KI,GD=ic_GD,GM=ic_GM,GT=IC$GT,
method=DP$kinship.algorithm,GTindex=DP$GTindex,LD=DP$LD,
bin.size=DP$bin.size,bin.selection=DP$bin.selection,alpha=DP$alpha,WS=DP$WS,
cutOff=DP$cutOff,p.threshold=DP$p.threshold,QTN.threshold=DP$QTN.threshold,
maf.threshold=DP$maf.threshold,method.GLM=DP$method.GLM,method.sub=DP$method.sub,
method.sub.final=DP$method.sub.final,method.bin=DP$method.bin,
DPP=DP$DPP,file.output=DP$file.output,Multi_iter=DP$Multi_iter,windowsize=DP$windowsize )
GWAS=myBus$GWAS
Pred=myBus$GPS
va=myBus$vg
ve=myBus$ve
h2=va/(va+ve)
mc=NULL
#mc=(exp(1)^(1/GWAS$P.value))/10000
bc=NULL
mp=NULL
#myP=1/(exp(10000*fm$tau2)
#print(str(GWAS))
TV=NULL
Compression=NULL
GVs=myBus$GVs
}
#print(ic_GD[1:10,1:10])
if(!DP$kinship.algorithm%in%c("FarmCPU","MLMM","Blink"))
{
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="GAPIT.Main")
Memory=GAPIT.Memory(Memory=Memory,Infor="GAPIT.Main")
GT=as.matrix(ic_GD[,1])
#print("!!!!!!!")
#print(DP$sangwich.top)
if(DP$PCA.total==0) ic_PCA=NULL
#print(dim(ic_PCA))
gapitMain <- GAPIT.Main(Y=ic_Y,GD=DP$GD[,-1],GM=DP$GM,KI=ic_KI,Z=Z,CV=DP$CV,CV.Inheritance=DP$CV.Inheritance,GP=DP$GP,GK=DP$GK,SNP.P3D=DP$SNP.P3D,kinship.algorithm=DP$kinship.algorithm,
bin.from=DP$bin.from,bin.to=DP$bin.to,bin.by=DP$bin.by,inclosure.from=DP$inclosure.from,inclosure.to=DP$inclosure.to,inclosure.by=DP$inclosure.by,
group.from=DP$group.from,group.to=DP$group.to,group.by=DP$group.by,kinship.cluster=DP$kinship.cluster,kinship.group=DP$kinship.group,name.of.trait=DP$name.of.trait,
file.path=DP$file.path,file.from=DP$file.from, file.to=DP$file.to, file.total=DP$file.total, file.fragment = DP$file.fragment, file.G=DP$file.G,file.Ext.G=DP$file.Ext.G,file.GD=DP$file.GD, file.GM=DP$file.GM, file.Ext.GD=DP$file.Ext.GD,file.Ext.GM=DP$file.Ext.GM,
SNP.MAF= DP$SNP.MAF,FDR.Rate = DP$FDR.Rate,SNP.FDR=DP$SNP.FDR,SNP.effect=DP$SNP.effect,SNP.impute=DP$SNP.impute,PCA.total=DP$PCA.total,GAPIT.Version=GAPIT.Version,
GT=GT, SNP.fraction = DP$SNP.fraction, seed =DP$ seed, BINS = DP$BINS,SNP.test=DP$SNP.test,DPP=DP$DPP, SNP.permutation=DP$SNP.permutation,
LD.chromosome=DP$LD.chromosome,LD.location=LD.location,LD.range=LD.range,SNP.CV=SNP.CV,SNP.robust=DP$SNP.robust,model=DP$model,
genoFormat="EMMA",hasGenotype=TRUE,byFile=FALSE,fullGD=TRUE,PC=DP$PC,GI=ic_GM,Timmer = DP$Timmer, Memory = DP$Memory,
sangwich.top=DP$sangwich.top,sangwich.bottom=DP$sangwich.bottom,QC=DP$QC,GTindex=DP$GTindex,LD=DP$LD,file.output=FALSE,cutOff=DP$cutOff, GAPIT3.output=DP$file.output,
Model.selection = DP$Model.selection, Create.indicator = DP$Create.indicator,
QTN=DP$QTN, QTN.round=DP$QTN.round,QTN.limit=DP$QTN.limit, QTN.update=QTN.update, QTN.method=DP$QTN.method, Major.allele.zero=DP$Major.allele.zero,NJtree.group=DP$NJtree.group,NJtree.type=DP$NJtree.type,plot.bin=DP$plot.bin,
QTN.position=DP$QTN.position,plot.style=DP$plot.style,SUPER_GS=DP$SUPER_GS)
#print(str(gapitMain))
GWAS=gapitMain$GWAS
GR=GAPIT.RandomModel(Y=ic_Y,X=DP$GD[,-1],GWAS=GWAS,CV=gapitMain$PC,cutOff=DP$cutOff,GT=IC$GT)
Pred=gapitMain$Pred
#print(head(Pred))
va=NA#gapitMain$vg
ve=NA#gapitMain$ve
h2=gapitMain$h2
mc=gapitMain$effect.snp
bc=gapitMain$effect.cv
mp=gapitMain$P
TV=gapitMain$TV
Compression=gapitMain$Compression
GVs=GR$GVs
}
myPower=NULL
#print(head(GWAS))
#print(DP$QTN.position)
if(!is.null(GWAS))myPower=GAPIT.Power(WS=DP$WS, alpha=DP$alpha, maxOut=DP$maxOut,seqQTN=DP$QTN.position,GM=DP$GM,GWAS=GWAS)
#print(str(myPower))
#print("GAPIT.III accomplished successfully for multiple traits. Results are saved")
return (list(GWAS=GWAS,Pred=Pred,FDR=myPower$FDR,Power=myPower$Power,
Power.Alpha=myPower$Power.Alpha,alpha=myPower$alpha,h2=h2,va=va,ve=ve,
mc=mc,bc=bc,mp=mp,TV=TV,Compression=Compression,
Timmer=Timmer,Memory=Memory,GVs=GVs))
}else{
#
# print("!!!!!!!!!")
# print(dim(DP$Y))
# print(dim(DP$GD))
# print(dim(DP$CV))
# print(dim(DP$PC))
gapitMain <- GAPIT.Main(Y=DP$Y,GD=DP$GD[,-1],GM=DP$GM,KI=DP$KI,Z=DP$Z,CV=DP$CV,CV.Inheritance=DP$CV.Inheritance,GP=DP$GP,GK=DP$GK,SNP.P3D=DP$SNP.P3D,kinship.algorithm=DP$kinship.algorithm,
bin.from=DP$bin.from,bin.to=DP$bin.to,bin.by=DP$bin.by,inclosure.from=DP$inclosure.from,inclosure.to=DP$inclosure.to,inclosure.by=DP$inclosure.by,
group.from=DP$group.from,group.to=DP$group.to,group.by=DP$group.by,kinship.cluster=DP$kinship.cluster,kinship.group=DP$kinship.group,name.of.trait=DP$name.of.trait,
file.path=DP$file.path,file.from=DP$file.from, file.to=DP$file.to, file.total=DP$file.total, file.fragment = DP$file.fragment, file.G=DP$file.G,file.Ext.G=DP$file.Ext.G,file.GD=DP$file.GD, file.GM=DP$file.GM, file.Ext.GD=DP$file.Ext.GD,file.Ext.GM=DP$file.Ext.GM,
SNP.MAF= DP$SNP.MAF,FDR.Rate = DP$FDR.Rate,SNP.FDR=DP$SNP.FDR,SNP.effect=DP$SNP.effect,SNP.impute=DP$SNP.impute,PCA.total=DP$PCA.total,GAPIT.Version=GAPIT.Version,
GT=DP$GT, SNP.fraction = DP$SNP.fraction, seed =DP$ seed, BINS = DP$BINS,SNP.test=DP$SNP.test,DPP=DP$DPP, SNP.permutation=DP$SNP.permutation,
LD.chromosome=DP$LD.chromosome,LD.location=LD.location,LD.range=LD.range,SNP.CV=SNP.CV,SNP.robust=DP$SNP.robust,model=DP$model,
genoFormat="EMMA",hasGenotype=TRUE,byFile=FALSE,fullGD=TRUE,PC=DP$PC,GI=DP$GI,Timmer = DP$Timmer, Memory = DP$Memory,GAPIT3.output=DP$file.output,
sangwich.top=DP$sangwich.top,sangwich.bottom=DP$sangwich.bottom,QC=DP$QC,GTindex=DP$GTindex,LD=DP$LD,file.output=FALSE,cutOff=DP$cutOff,
Model.selection = DP$Model.selection, Create.indicator = DP$Create.indicator,
QTN=DP$QTN, QTN.round=DP$QTN.round,QTN.limit=DP$QTN.limit, QTN.update=QTN.update, QTN.method=DP$QTN.method, Major.allele.zero=DP$Major.allele.zero,NJtree.group=DP$NJtree.group,NJtree.type=DP$NJtree.type,plot.bin=DP$plot.bin,
QTN.position=DP$QTN.position,plot.style=DP$plot.style,SUPER_GS=DP$SUPER_GS)
#print(str(gapitMain))
GWAS=gapitMain$GWAS
#print(head(GWAS))
Pred=gapitMain$Pred
#print(head(Pred))
va=NA#gapitMain$vg
ve=NA#gapitMain$ve
h2=gapitMain$h2
mc=gapitMain$effect.snp
bc=gapitMain$effect.cv
mp=gapitMain$P
Compression=gapitMain$Compression
return (list(GWAS=GWAS,Pred=Pred,FDR=NULL,Power=NULL,
Power.Alpha=NULL,alpha=NULL,h2=h2,va=va,ve=ve,Compression=Compression,
mc=mc,bc=bc,mp=mp,TV=gapitMain$TV,
Timmer=Timmer,Memory=Memory))
}#end of SNP.TEST
} #end of GAPIT.SS function
#=============================================================================================
`GAPIT.SUPER.FastMLM` <-
function(ys, xs, vg, delta, Z = NULL, X0 = NULL, snp.pool=NULL,LD=0.01,method="FaST") {
#Input: ys, xs, vg, delta, Z, X0, snp.pool
#Output: GWAS
#Authors: Qishan Wang, Feng Tian and Zhiwu Zhang
#Last update: April 16, 2012
################################################################################
#print("GAPIT.SUPER.FastMLM started")
#print("dimension of ys,xs,X0 and snp.pool")
#print(length(ys))
#print(dim(xs))
#print(dim(X0))
#print(dim(snp.pool))
#print((LD))
#Set data to the require format
ys=unlist(ys)
if(is.null(dim(ys)) || ncol(ys) == 1) ys <- matrix(ys, 1, length(ys))
if(is.null(dim(xs)) || ncol(xs) == 1) xs <- matrix(xs, 1, length(xs))
if(is.null(X0)) X0 <- matrix(1, nrow(snp.pool), 1)
#Exract data size
g <- nrow(ys)
n <- nrow(xs) ##### generaol nrow(xs)=nrow(U1) rivised by qishan 2012.4.16
m <- ncol(xs)
t <- nrow(xs)
q0 <- ncol(X0)
q1 <- q0 + 1
#Allocate space
dfs <- matrix(nrow = m, ncol = g)
stats <- matrix(nrow = m, ncol = g)
ps <- matrix(nrow = m, ncol = g)
betavalue <- matrix(nrow = m, ncol = g)
####################
if(method=="SUPER"){
LDsqr=sqrt(LD)
##################
#Iteration on trait (j) and SNP (i)
for(j in 1:g)
{
for (i in 1:m)
{
if((i >0)&(floor(i/500)==i/500)) print(paste("SNP: ",i," ",sep=""))
#No variation on the SNP
if(min(xs[,i])==max(xs[,i]))
{
dfs[i,j] <- n - q1
betavalue[i,j]=0
stats[i,j] <- 0
}
#The SNP has variation
if(min(xs[,i])!=max(xs[,i]))
{
#SUPER
snp.corr=cor(xs[,i],snp.pool)
index.k=which( abs(snp.corr)<=LDsqr )
#handler of snp correlated with all QTNs
if(length(index.k)<2){
index.k=1:length(snp.corr) #keep going to have them all
#print("warning: there is a snp correlated with all QTNs")
}
K.X= snp.pool[,index.k]
####################
K.X.svd= svd(K.X) ###start 2012.4.16 by qishan
d=K.X.svd$d
d=d[d>1e-8]
d=d^2
U1=K.X.svd$u
U1=U1[,1:length(d)] ### end 2012.4.16 by qishan
n<-nrow(U1)
I= diag(1,nrow(U1))
################ get iXX
X <- cbind(X0, xs[,i]) ####marker by column
U <- U1*matrix(sqrt(1/(d + delta)), nrow(U1), length(d), byrow = TRUE)
Xt <- crossprod(U, X)
XX1<- crossprod(Xt, Xt)
XX2<- crossprod((I-tcrossprod(U1,U1))%*%X,(I-tcrossprod(U1,U1))%*%X)/delta
#iXX<-solve(XX1+XX2)
iXX <- try(solve(XX1+XX2),silent=T)
if(inherits(iXX, "try-error")){
iXX <- ginv(XX1+XX2)
}
################# end get ixx
################ begin get beta
################
#######get beta compnents 1
#U1TX=t(U1)%*%X
U1TX=crossprod(U1,X)
beta1=0
for(ii in 1:length(d)){
one=matrix(U1TX[ii,], nrow=1)
dim(one)
#beta=t(one)%*%one/(d[ii]+delta)
beta=crossprod(one,one)/(d[ii]+delta)
beta1= beta1+beta
}
#######get beta components 2
#IUX=(I-U1%*%t(U1))%*%X
IUX=(I-tcrossprod(U1,U1))%*%X
beta2=0
for(ii in 1:nrow(U1)){
one=matrix(IUX[ii,], nrow=1)
dim(one)
beta=t(one)%*%one
beta2= beta2+beta
}
beta2<-beta2/delta
#######get b3
#U1TY=t(U1)%*%ys[j,]
U1TY=crossprod(U1,ys[j,])
beta3=0
for(ii in 1:length(d)){
one1=matrix(U1TX[ii,], nrow=1)
one2=matrix(U1TY[ii,], nrow=1)
beta=crossprod(one1,one2)/(d[ii]+delta)
beta3= beta3+beta
}
###########get beta4
#IUY=(I-U1%*%t(U1))%*%ys[j,]
IUY=(I-tcrossprod(U1,U1))%*%ys[j,]
beta4=0
for(ii in 1:nrow(U1)){
one1=matrix(IUX[ii,], nrow=1)
one2=matrix(IUY[ii,], nrow=1)
#beta=t(one1)%*%one2
beta=crossprod(one1,one2)
beta4= beta4+beta
}
beta4<-beta4/delta
#######get final beta
beta=ginv(beta1+beta2)%*%(beta3+beta4)
##############
################ end get beta
betavalue[i,j]=beta[q1,1]
stats[i,j] <- beta[q1,1]/sqrt(iXX[q1, q1] * vg)
dfs[i,j] <- n - q1
} #end of SNP variation stutus detection
} #loop for markers
#print("Calculating p-values...")
ps[,j] <- 2 * pt(abs(stats[,j]), dfs[,j], lower.tail = FALSE)
} #end of loop on traits
return(list(beta=betavalue, ps = ps, stats = stats, dfs = dfs,effect=betavalue))
} #Enf of SUPERMLM
#######################
if(method=="FaST"){
K.X.svd= svd(snp.pool) ###start 2012.4.16 by qishan
d=K.X.svd$d
d=d[d>1e-8]
d=d^2
U1=K.X.svd$u
U1=U1[,1:length(d)] ### end 2012.4.16 by qishan
n<-nrow(U1)
I= diag(1,nrow(U1))
U <- U1*matrix(sqrt(1/(d + delta)), nrow(U1), length(d), byrow = TRUE)
##################
#Iteration on trait (j) and SNP (i)
for(j in 1:g)
{
for (i in 1:m)
{
if((i >0)&(floor(i/500)==i/500)) print(paste("SNP: ",i," ",sep=""))
#No variation on the SNP
if(min(xs[,i])==max(xs[,i]))
{
dfs[i,j] <- n - q1
betavalue[i,j]=0
stats[i,j] <- 0
}
#The SNP has variation
if(min(xs[,i])!=max(xs[,i]))
{
#SUPER
####################
K.X.svd= svd(snp.pool) ###start 2012.4.16 by qishan
d=K.X.svd$d
d=d[d>1e-8]
d=d^2
U1=K.X.svd$u
U1=U1[,1:length(d)] ### end 2012.4.16 by qishan
n<-nrow(U1)
I= diag(1,nrow(U1))
################ get iXX
X <- cbind(X0, xs[,i]) ####marker by column
U <- U1*matrix(sqrt(1/(d + delta)), nrow(U1), length(d), byrow = TRUE)
Xt <- crossprod(U, X)
XX1<- crossprod(Xt, Xt)
XX2<- crossprod((I-tcrossprod(U1,U1))%*%X,(I-tcrossprod(U1,U1))%*%X)/delta
iXX <- try(solve(XX1+XX2),silent=T)
if(inherits(iXX, "try-error")){
iXX <- ginv(XX1+XX2)
}
################# end get ixx
################ begin get beta
#######get beta compnents 1
#U1TX=t(U1)%*%X
U1TX=crossprod(U1,X)
beta1=0
for(ii in 1:length(d)){
one=matrix(U1TX[ii,], nrow=1)
dim(one)
beta=crossprod(one,one)/(d[ii]+delta)
beta1= beta1+beta
}
#######get beta components 2
IUX=(I-tcrossprod(U1,U1))%*%X
beta2=0
for(ii in 1:nrow(U1)){
one=matrix(IUX[ii,], nrow=1)
dim(one)
beta=crossprod(one,one)
beta2= beta2+beta
}
beta2<-beta2/delta
#######get b3
#U1TY=t(U1)%*%ys[j,]
U1TY=crossprod(U1,ys[j,])
beta3=0
for(ii in 1:length(d)){
one1=matrix(U1TX[ii,], nrow=1)
one2=matrix(U1TY[ii,], nrow=1)
#beta=t(one1)%*%one2/(d[ii]+delta)
beta=crossprod(one1,one2)/(d[ii]+delta)
beta3= beta3+beta
}
###########get beta4
#IUY=(I-U1%*%t(U1))%*%ys[j,]
IUY=(I-tcrossprod(U1,U1))%*%ys[j,]
beta4=0
for(ii in 1:nrow(U1)){
one1=matrix(IUX[ii,], nrow=1)
one2=matrix(IUY[ii,], nrow=1)
#beta=t(one1)%*%one2
beta=crossprod(one1,one2)
beta4= beta4+beta
}
beta4<-beta4/delta
#######get final beta
beta=ginv(beta1+beta2)%*%(beta3+beta4)
##############
################ end get beta
betavalue[i,j]=beta[q1,1]
stats[i,j] <- beta[q1,1]/sqrt(iXX[q1, q1] * vg)
dfs[i,j] <- n - q1
} #end of SNP variation stutus detection
} #loop for markers
#print("Calculating p-values...")
ps[,j] <- 2 * pt(abs(stats[,j]), dfs[,j], lower.tail = FALSE)
} #end of loop on traits
return(list(beta=betavalue, ps = ps, stats = stats, dfs = dfs,effect=betavalue))
} #Enf of FastMLM
}####end function
#=============================================================================================
`GAPIT.SUPER.GS`<-
function(Y=Y[,c(1,trait)],G=NULL,GD=NULL,GM=NULL,KI=NULL,Z=NULL,CV=NULL,GK=GK,kinship.algorithm=kinship.algorithm,
bin.from=bin.from,bin.to=bin.to,bin.by=bin.by,inclosure.from=inclosure.from,inclosure.to=inclosure.to,inclosure.by=inclosure.by,
group.from=group.from,group.to=group.to,group.by=group.by,kinship.cluster=kinship.cluster,kinship.group=kinship.group,name.of.trait=traitname,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF= SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,PCA.total=PCA.total,GAPIT.Version=GAPIT.Version,
GT=GT, SNP.fraction = SNP.fraction, seed = seed, BINS = BINS,SNP.test=SNP.test,DPP=DPP, SNP.permutation=SNP.permutation,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,SNP.CV=SNP.CV,SNP.robust=SNP.robust,model=model,
genoFormat=genoFormat,hasGenotype=hasGenotype,byFile=byFile,fullGD=fullGD,PC=PC,GI=GI,Timmer = Timmer, Memory = Memory,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,QC=QC,GTindex=GTindex,LD=LD,file.output=file.output,cutOff=cutOff
){
#Object: To perform GPS with SUPER and Compress method
#Designed by Zhiwu Zhang
#Writen by Jiabo Wang
#Last update: Novber 6, 2015
######################################################
print("--------------------- Welcome to GAPIT SUPER GS----------------------------")
Timmer=GAPIT.Timmer(Infor="GAPIT.SUPER.GS")
Memory=GAPIT.Memory(Infor="GAPIT.SUPER.GS")
if(!require(EMMREML)) install.packages("EMMREML")
library(EMMREML)
shortcut=FALSE
LL.save=1e10
#In case of null Y and null GP, return genotype only
thisY=Y[,2]
thisY=thisY[!is.na(thisY)]
if(length(thisY) <3){
shortcut=TRUE
}else{
if(var(thisY) ==0) shortcut=TRUE
}
if(shortcut){
print(paste("Y is empty. No GWAS/GS performed for ",name.of.trait,sep=""))
return (list(compression=NULL,kinship.optimum=NULL, kinship=KI,PC=PC,GWAS=NULL, GPS=NULL,Pred=NULL, REMLs=NULL,Timmer=Timmer,Memory=Memory))
}
print("------------Examining data (QC)------------------------------------------")
if(is.null(Y)) stop ("GAPIT says: Phenotypes must exist.")
if(is.null(KI)&missing(GD) & kinship.algorithm!="SUPER") stop ("GAPIT says: Kinship is required. As genotype is not provided, kinship can not be created.")
if(is.null(GD) & is.null(GT)) {
GT=as.matrix(Y[,1])
GD=matrix(1,nrow(Y),1)
GI=as.data.frame(matrix(0,1,3) )
colnames(GI)=c("SNP","Chromosome","Position")
}
#merge CV with PC
#print(dim(CV))
#if(PCA.total>0&!is.null(CV))CV=GAPIT.CVMergePC(CV,PC)
#if(PCA.total>0&is.null(CV))CV=PC
#for GS merge CV with GD name
#print("!!!!!!")
#print(dim(CV))
# print(head(GT))
# print(head(GI))
# if (is.null(CV))
# {my_allCV=CV
# }else{
# taxa_GD=GT
# my_allCV=CV[order(CV[,1]),]
# my_allCV=my_allCV[my_allCV[,1]%in%taxa_GD,]
# #print(dim(my_allCV))
# }
my_allCV=CV
#print(dim(my_allCV))
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & is.null(Z)){
taxa=as.character(Y[,1])
Z=as.data.frame(diag(1,nrow(Y)))
Z=rbind(taxa,Z)
taxa=c('Taxa',as.character(taxa))
Z=cbind(taxa,Z)
}
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & !is.null(Z))
{
if(nrow(Z)-1<nrow(Y)) Z=GAPIT.ZmatrixFormation(Z=Z,Y=Y)
}
noCV=FALSE
if(is.null(CV)){
noCV=TRUE
CV=Y[,1:2]
CV[,2]=1
colnames(CV)=c("taxa","overall")
}
#Remove duplicat and integragation of data
print("QC is in process...")
CVI <- CV
if(QC)
{
#print(colnames(KI)[53:62])
qc <- GAPIT.QC(Y=Y,KI=KI, GT=GT,CV=CV,Z=Z,GK=GK)
GTindex=qc$GTindex
Y=qc$Y
KI=qc$KI
CV=qc$CV
Z=qc$Z
GK=qc$GK
my_taxa=as.character(KI[,1])
my_allKI=KI
#print(dim(CV))
}
print("The value of QC is")
print(QC)
rm(qc)
gc()
print("------------Examining data (QC) done-------------------------------------")
super_pass=FALSE
SUPER_myKI=NULL
SUPER_optimum_GD=NULL
if (!is.null(sangwich.top)) super_pass=TRUE
if(super_pass)
{
print("-------------------start SUPER BREAD-----------------------------------")
#Create GK if not provided
#print(memory.size())
if(is.null(GK)){
nY=floor(nrow(Y)*.9)
nG=ncol(GD)
if(nG>nY){snpsam=sample(1:nG,nY)}else{snpsam=1:nG}
GK=GD[GTindex,snpsam]
SNPVar=apply(as.matrix(GK),2,var)
#print(snpsam)
if (snpsam==1)stop ("GAPIT says: SUPER_GS must putin GD and GM.")
GK=GK[,SNPVar>0]
GK=cbind(as.data.frame(GT[GTindex]),as.data.frame(GK)) #add taxa
}
#print(head(CV))
#myGD=cbind(as.data.frame(GT),as.data.frame(GD))
file.output.temp=file.output
file.output=FALSE
# print(memory.size())
GP=GAPIT.Bread(Y=Y,CV=CV,Z=Z,KI=KI,GK=GK,GD=cbind(as.data.frame(GT),as.data.frame(GD)),GM=GI,method=sangwich.top,GTindex=GTindex,LD=LD,file.output=file.output)$GWAS
file.output=file.output.temp
# print(memory.size())
GK=NULL
if(inclosure.to>nrow(Y)) ##########removed by Jiabo Wang ,unlimited number of inclosures
{
inclosure.to=nrow(Y)-1
print("the number of choosed inclosure is more than number of individuals")
print("Set the number of choosed incolosure max equal to individuals")
}
if(inclosure.from>inclosure.to) ##########removed by Jiabo Wang ,unlimited number of inclosures
{
inclosure.from=inclosure.to
}
bin.level=seq(bin.from,bin.to,by=bin.by)
inclosure=seq(inclosure.from,inclosure.to,by=inclosure.by)
#print(inclosure)
e=1 #################################number of bins and inclosure
count=0
num_selection=length(bin.level)*length(inclosure)
SUPER_selection=matrix(,num_selection,6)
colnames(SUPER_selection)=c("bin","pseudo_QTNs","Max_pQTNs","REML","VA","VE")
#for (bin in bin.level){bin=bin.level[e]}
#for (inc in inclosure){inc=inclosure[e]}
for (bin in bin.level){
for (inc in inclosure){
count=count+1
mySpecify=GAPIT.Specify(GI=GI,GP=GP,bin.size=bin,inclosure.size=inc)
SNP.QTN=mySpecify$index
num_pseudo_QTN=length(mySpecify$CB)
num_bins=mySpecify$num_bins
#print(paste("bin---",bin,"---inc---",inc,sep=""))
GK=GD[GTindex,SNP.QTN]
SUPER_GD=GD[,SNP.QTN]
SNPVar=apply(as.matrix(GK),2,var)
GK=GK[,SNPVar>0]
SUPER_GD=SUPER_GD[,SNPVar>0]
GK=cbind(as.data.frame(GT[GTindex]),as.data.frame(GK)) #add taxa
SUPER_GD=cbind(as.data.frame(GT),as.data.frame(SUPER_GD)) #add taxa
myBurger=GAPIT.Burger(Y=Y,CV=CV,GK=GK) #modifed by Jiabo Wang
myREML=myBurger$REMLs
myVG=myBurger$vg
myVE=myBurger$ve
SUPER_selection[count,1]=bin
SUPER_selection[count,2]=num_pseudo_QTN
SUPER_selection[count,3]=num_bins
SUPER_selection[count,4]=myREML
SUPER_selection[count,5]=myVG
SUPER_selection[count,6]=myVE
#print(SUPER_selection[count,])
if(count==1){
GK.save=GK
LL.save=myREML
SUPER_optimum_GD=SUPER_GD ########### get SUPER GD
}else{
if(myREML<LL.save){
GK.save=GK
LL.save=myREML
SUPER_optimum_GD=SUPER_GD ########### get SUPER GD
}
}
if (num_bins==num_pseudo_QTN) break
}# bin end
}# inc end
SUPER_selection<-SUPER_selection[!is.na(SUPER_selection[,1]),]
print(SUPER_selection)
print("-----select optimum pseudo QTNs from all the bins-------")
if(is.null(dim(SUPER_selection)))
{optimum_SUPER=SUPER_selection
}else{
optimum_SUPER=SUPER_selection[which(as.numeric(SUPER_selection[,4])==min(as.numeric(SUPER_selection[,4]))),]
}
print(optimum_SUPER)
########################BUILD SUPER KINSHIP
##########################################################
colnames(SUPER_optimum_GD)=c("taxa",colnames(SUPER_optimum_GD)[-1])
SUPER_taxa=as.character(SUPER_optimum_GD[,1])
SUPER_X=SUPER_optimum_GD[,-1]
if(kinship.algorithm=="Loiselle")SUPER_myKI_test= GAPIT.kinship.loiselle(snps=t(as.matrix(.5*(SUPER_optimum_GD[,-1]))), method="additive", use="all")
# if(kinship.algorithm=="VanRaden")SUPER_myKI_test= GAPIT.kinship.VanRaden(snps=as.matrix(SUPER_optimum_GD[,-1]))
if(kinship.algorithm=="Zhang")SUPER_myKI_test= GAPIT.kinship.ZHANG(snps=as.matrix(SUPER_optimum_GD[,-1]))
if(!kinship.algorithm=="Loiselle"|!kinship.algorithm=="Zhang")SUPER_myKI_test= GAPIT.kinship.VanRaden(snps=as.matrix(SUPER_optimum_GD[,-1]))
SUPER_myKI_test=GAPIT.kinship.VanRaden(snps=as.matrix(SUPER_optimum_GD[,-1])) # build kinship
colnames(SUPER_myKI_test)=SUPER_taxa
SUPER_myKI=cbind(SUPER_taxa,as.data.frame(SUPER_myKI_test))
print("select optimum number of marker effect in GD")
print(dim(SUPER_optimum_GD))
#print(SUPER_optimum_GD[1:5,1:5])
######################################GOIN TO NEW CBLUP
Z=NULL
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & is.null(Z)){
taxa=as.character(SUPER_optimum_GD[,1])
Z=as.data.frame(diag(1,nrow(SUPER_optimum_GD)))
Z=rbind(taxa,Z)
taxa=c('Taxa',as.character(taxa))
Z=cbind(taxa,Z)
}
if(kinship.algorithm!="None" & kinship.algorithm!="SUPER" & !is.null(Z))
{
if(nrow(Z)-1<nrow(Y)) Z=GAPIT.ZmatrixFormation(Z=Z,Y=Y)
}
print("QC is in process...")
GK=NULL
CVI <- CV
if(QC)
{
qc <- GAPIT.QC(Y=Y,KI=SUPER_myKI, GT=GT,CV=CV,Z=Z,GK=GK)
GTindex=qc$GTindex
Y=qc$Y
KI=qc$KI
CV=qc$CV
Z=qc$Z
GK=qc$GK
}
rm(qc)
gc()
}# super_pass end
nk=1000000000
if(!is.null(KI)) nk=min(nk,nrow(KI))
if(!is.null(GK)) nk=min(nk,nrow(GK))
if(!is.null(KI))
{
if(group.to>nk) {
#group.to=min(nrow(KI),length(GTindex)) #maximum of group is number of rows in KI
group.to=nk #maximum of group is number of rows in KI
warning("The upper bound of groups is too high. It was set to the size of kinship!")
}
if(group.from>nk){
group.from=nk
warning("The lower bound of groups is too high. It was set to the size of kinship!")
}
}
if(!is.null(CV)){
if(group.to<=ncol(CV)+1) {
#The minimum of group is number of columns in CV
group.from=ncol(CV)+2
group.to=ncol(CV)+2
warning("The upper bound of groups (group.to) is not sufficient. both boundries were set to their minimum and GLM is performed!")
}
}
GROUP=seq(group.to,group.from,by=-group.by)#The reverse order is to make sure to include full model
if(missing("kinship.cluster")) kinship.cluster=c("ward", "single", "complete", "average", "mcquitty", "median", "centroid")
if(missing("kinship.group")) kinship.group=c("Mean", "Max", "Min", "Median")
numSetting=length(GROUP)*length(kinship.cluster)*length(kinship.group)
ys=as.matrix(Y[2])
X0=as.matrix(CV[,-1])
if(min(X0[,1])!=max(X0[,1])) X0 <- cbind(1, X0) #do not add overall mean if X0 has it already at first column
hold_Z=Z
# library("EMMREML")
order_count=0
storage_reml=NULL
Compression=matrix(,numSetting,6)
colnames(Compression)=c("Type","Cluster","Group","REML","VA","VE")
for (group in GROUP)
{
for (ca in kinship.cluster)
{
for (kt in kinship.group)
{
#if(group=1) group=2
#if(!optOnly) {print("Compressing and Genome screening..." )}
order_count=order_count+1
if(order_count==1)print("-------Mixed model with Kinship-----------------------------")
if(group<ncol(X0)+1) group=2 # the emma function (emma.delta.REML.dLL.w.Z) does not allow K has dim less then CV. turn to GLM (group=1)
cp <- GAPIT.Compress(KI=KI,kinship.cluster=ca,kinship.group=kt,GN=group,Timmer=Timmer,Memory=Memory)
bk <- GAPIT.Block(Z=hold_Z,GA=cp$GA,KG=cp$KG)
zc <- GAPIT.ZmatrixCompress(Z=hold_Z,GAU =bk$GA)
zrow=nrow(zc$Z)
zcol=ncol(zc$Z)-1
K = as.matrix(bk$KW)
#if (nrow(as.matrix(bk$KW))==1)
Z=matrix(as.numeric(as.matrix(zc$Z[,-1])),nrow=zrow,ncol=zcol)
if(is.null(dim(ys)) || ncol(ys) == 1) ys <- matrix(ys, 1, length(ys))
if(is.null(X0)) X0 <- matrix(1, ncol(ys), 1)
#handler of special Z and K
if(!is.null(Z)){ if(ncol(Z) == nrow(Z)) Z = NULL }
if(!is.null(K)) {if(length(K)<= 1) K = NULL}
X <- X0 #covariate variables such as population structure
j=1
if (is.null(Z)) Z=diag(x=1,nrow(K),ncol(K))
if (group==1) K=1
#print(head(X))
emma_test <- emmreml(as.numeric(ys), X=as.matrix(X), K=as.matrix(K), Z=Z,varbetahat=FALSE,varuhat=FALSE, PEVuhat=FALSE, test=FALSE)
print(paste(order_count, "of",numSetting,"--","Vg=",round(emma_test$Vu,4), "VE=",round(emma_test$Ve,4),"-2LL=",round(-2*emma_test$loglik,2), " Clustering=",ca," Group number=", group ," Group kinship=",kt,sep = " "))
emma_test_reml=-2*emma_test$loglik
storage_reml=append(storage_reml,-2*emma_test$loglik)
Compression[order_count,1]=kt
Compression[order_count,2]=ca
Compression[order_count,3]=group
Compression[order_count,4]=emma_test_reml
Compression[order_count,5]=emma_test$Vu
Compression[order_count,6]=emma_test$Ve
if(order_count==1){
save_remle=emma_test_reml
optimum_group=group
optimum_Clustering=ca
optimum_groupK=kt
}else{
if(emma_test_reml<save_remle){
save_remle=emma_test_reml
optimum_group=group
optimum_Clustering=ca
optimum_groupK=kt
}
}
} # kt end
} # ka end
} # group end
print(Compression)
if(optimum_group==1)
{
optimum_group=2
}
#print(colnames(KI)[53:62])
cp <- GAPIT.Compress(KI=KI,kinship.cluster=optimum_Clustering,kinship.group=optimum_groupK,GN=optimum_group,Timmer=Timmer,Memory=Memory)
bk <- GAPIT.Block(Z=hold_Z,GA=cp$GA,KG=cp$KG)
zc <- GAPIT.ZmatrixCompress(Z=hold_Z,GAU =bk$GA)
zrow=nrow(zc$Z)
zcol=ncol(zc$Z)-1
K = as.matrix(bk$KW)
Z=matrix(as.numeric(as.matrix(zc$Z[,-1])),nrow=zrow,ncol=zcol)
if(is.null(dim(ys)) || ncol(ys) == 1) ys <- matrix(ys, 1, length(ys))
if(is.null(X0)) X0 <- matrix(1, ncol(ys), 1)
X <- X0 #covariate variables such as population structure
if (is.null(Z)) Z=diag(x=1,nrow(K),ncol(K))
# print(my_allCV)
if (is.null(my_allCV)){my_allX=matrix(1,length(my_taxa),1)
}else{
# my_allX=as.matrix(my_allCV[,-1])
my_allX=cbind(1,as.matrix(my_allCV[,-1]))
}
emma_REMLE <- emmreml(y=as.numeric(ys), X=as.matrix(X), K=as.matrix(K), Z=Z,varbetahat=TRUE,varuhat=TRUE, PEVuhat=TRUE, test=TRUE)
#print(head(emma_REMLE$uhat))
#print(emma_REMLE$uhat[53:62])
emma_BLUE=as.matrix(my_allX)%*%as.matrix(emma_REMLE$betahat)
emma_BLUE=as.data.frame(cbind(my_taxa,emma_BLUE))
colnames(emma_BLUE)=c("Taxa","emma_BLUE")
gs <- GAPIT.GS(KW=bk$KW,KO=bk$KO,KWO=bk$KWO,GAU=bk$GAU,UW=cbind(emma_REMLE$uhat,emma_REMLE$PEVuhat))
#print(head(gs$BLUP))
#print(head(emma_BLUE))
BB= merge(gs$BLUP, emma_BLUE, by.x = "Taxa", by.y = "Taxa")
#print(head(BB))
prediction=as.matrix(BB$BLUP)+as.numeric(as.vector(BB$emma_BLUE))
all_gs=cbind(BB,prediction)
colnames(all_gs)=c("Taxa","Group","RefInf","ID","BLUP","PEV","BLUE","Prediction")
#print(head(all_gs))
#print(model)
write.csv(all_gs,paste("GAPIT.",model,".Pred.result.csv",sep=""), row.names = FALSE,col.names = TRUE)
print("GAPIT SUPER GS completed successfully for multiple traits. Results are saved")
return (list(GPS=BB,Pred=all_gs,Compression=Compression,kinship=my_allKI,SUPER_kinship=SUPER_myKI,SUPER_GD=SUPER_optimum_GD ,PC=my_allCV,Timmer=Timmer,Memory=Memory,GWAS=NULL ))
}
`GAPIT.Specify` <-
function(GI=NULL,GP=NULL,bin.size=10000000,inclosure.size=NULL,MaxBP=1e10){
#Object: To get indicator (TURE or FALSE) for GI based on GP
#Straitegy
# 1.set bins for all snps in GP
# 2.keep the snp with smallest P value in each bin, record SNP ID
# 3.Search GI for SNP with SNP ID from above
# 4.return the position for SNP selected
#Input:
#GI: Data frame with three columns (SNP name, chr and base position)
#GP: Data frame with seven columns (SNP name, chr and base position, P, MAF,N,effect)
#Output:
#theIndex: a vector indicating if the SNPs in GI belong to QTN or not)
#Authors: Zhiwu Zhang
#Last update: September 24, 2011
##############################################################################################
#print("Specification in process...")
if(is.null(GP))return (list(index=NULL,BP=NULL))
#set inclosure bin in GP
#Create SNP ID: position+CHR*MaxBP
ID.GP=as.numeric(as.vector(GP[,3]))+as.numeric(as.vector(GP[,2]))*MaxBP
#Creat bin ID
bin.GP=floor(ID.GP/bin.size )
#Create a table with bin ID, SNP ID and p value (set 2nd and 3rd NA temporately)
binP=as.matrix(cbind(bin.GP,NA,NA,ID.GP,as.numeric(as.vector(GP[,4]))) )
n=nrow(binP)
#Sort the table by p value and then bin ID (e.g. sort p within bin ID)
binP=binP[order(as.numeric(as.vector(binP[,5]))),] #sort on P alue
binP=binP[order(as.numeric(as.vector(binP[,1]))),] #sort on bin
#set indicator (use 2nd 3rd columns)
binP[2:n,2]=binP[1:(n-1),1]
binP[1,2]=0 #set the first
binP[,3]= binP[,1]-binP[,2]
#Se representives of bins
ID.GP=binP[binP[,3]>0,]
#Choose the most influencial bins as estimated QTNs
#Handler of single row
if(is.null(dim(ID.GP))) ID.GP=matrix(ID.GP,1,length(ID.GP))
ID.GP=ID.GP[order(as.numeric(as.vector(ID.GP[,5]))),] #sort on P alue
#Handler of single row (again after reshape)
if(is.null(dim(ID.GP))) ID.GP=matrix(ID.GP,1,length(ID.GP))
index=!is.na(ID.GP[,4])
ID.GP=ID.GP[index,4] #must have chr and bp information, keep SNP ID only
num_bins=NULL
if(!is.null(inclosure.size) ) {
if(!is.na(inclosure.size)){
avaiable=min(inclosure.size,length(ID.GP))
#print("inclosure.size length(ID.GP) avaiable")
#print(inclosure.size)
#print(length(ID.GP))
num_bins=length(ID.GP) # create number of all bins
#print(avaiable)
if(avaiable==0){
ID.GP=-1
}else{
ID.GP=ID.GP[1:avaiable] #keep the top ones selected
}
#print("ID.GP")
#print(ID.GP)
#problem here ID.GP[1:0]==ID.GP[1:1]
}
}
#create index in GI
theIndex=NULL
if(!is.null(GI)){
ID.GI=as.numeric(as.vector(GI[,3]))+as.numeric(as.vector(GI[,2]))*MaxBP
#print("ID.GI")
#print(ID.GI)
theIndex=ID.GI %in% ID.GP
}
#print("Specification in process done")
myList=list(index=theIndex,CB=ID.GP)
return (list(index=theIndex,CB=ID.GP,num_bins=num_bins))
} #end of GAPIT.Specify
#=============================================================================================
`GAPIT.Table` <-
function(final.table = final.table, name.of.trait = name.of.trait,SNP.FDR=1){
#Object: Make and export a table of summary information from GWAS
#Output: A table summarizing GWAS results
#Authors: Alex Lipka and Zhiwu Zhang
# Last update: May 10, 2011
##############################################################################################
#Filter SNPs by FDR
index=(final.table[,7]<=SNP.FDR)
final.table=final.table[index,]
#Export this summary table as an excel file
write.table(final.table, paste("GAPIT.", name.of.trait, ".GWAS.Results.csv", sep = ""), quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
#print("GAPIT.Table accomplished successfully!")
} #GAPIT.Table ends here
#=============================================================================================
`GAPIT.Timmer` <-
function(Timmer=NULL,Infor){
#Object: To report current time
#Output: Timmer
#Authors: Zhiwu Zhang
# Last update: may 8, 2011
##############################################################################################
Time<- Sys.time()
if(is.null(Timmer)) {
Elapsed=0
Timmer=cbind(Infor,Time,Elapsed)
}else{
Elapsed=0
Timmer.current=cbind(Infor,Time,Elapsed)
Timmer=rbind(Timmer,Timmer.current)
Timmer[nrow(Timmer),3]=as.numeric(as.matrix(Timmer[nrow(Timmer),2]))-as.numeric(as.matrix(Timmer[nrow(Timmer)-1,2]))
}
#print(paste('Time used: ', Timmer[nrow(Timmer),3], ' seconds for ',Infor,sep="" ))
return (Timmer)
}#end of GAPIT.Timmer function
#=============================================================================================
`GAPIT.ZmatrixCompress` <-
function(Z,GAU){
#Object: To assign the fraction of a individual belonging to a group
#Output: Z
#Authors: Zhiwu Zhang
# Last update: April 14, 2011
##############################################################################################
#Extraction of GAU coresponding to Z, sort GAU rowwise to mach columns of Z, and make design matrix
#print("GAPIT.ZmatrixCompress")
#print(dim(Z))
#print(dim(GAU))
effect.Z=as.matrix(Z[1,-1])
effect.GAU=as.matrix(GAU[,1])
taxa=as.data.frame(Z[-1,1])
GAU0=GAU[effect.GAU%in%effect.Z,]
order.GAU=order(GAU0[,1])
GAU1 <- GAU0[order.GAU,]
#id.1=GAU1[which(GAU1[,3]==1),4]
id.1=GAU1[which(GAU1[,3]<2),4]
n=max(as.numeric(as.vector(id.1)))
x=as.numeric(as.matrix(GAU1[,4]))
DS=diag(n)[x,]
#sort Z column wise
order.Z=order(effect.Z)
Z=Z[-1,-1]
Z <- Z[,order.Z]
#Z matrix from individual to group
#Z1.numeric <- as.numeric(as.matrix(Z))
Z <- matrix(as.numeric(as.matrix(Z)), nrow = nrow(Z), ncol = ncol(Z))
Z=Z%*%DS
#Z3=data.frame(cbind(as.character(Z[-1,1]),Z2))
Z=data.frame(cbind(taxa,Z))
#Z=Z3[order(Z3[,1]),]
Z=Z[order(as.matrix(taxa)),]
#print("GAPIT.ZmatrixCompress accomplished successfully!")
return(list(Z=Z))
}#The function GAPIT.ZmatrixCompress ends here
#=============================================================================================
`GAPIT.ZmatrixFormation` <-
function(Z,Y){
#Object: To expande the proportion Z to final Z
#Output: Z
#Authors: Zhiwu Zhang
# Last update: April 22, 2011
##############################################################################################
#split individuals in Y to the ones that are given Z and the one not
taxa.Z=as.matrix(Z[-1,1])
taxa.Y=as.matrix(Y[,1])
taxa.diff=setdiff(taxa.Y,taxa.Z)
taxa.I=as.matrix(taxa.Y[match(taxa.diff,taxa.Y,nomatch = 0)])
taxa.Z.col=as.matrix(Z[1,-1])
#Create final Z with zero block and identity block
Z0=matrix(data=0,nrow=nrow(taxa.Z),ncol=nrow(taxa.I))
Z1=diag(1,nrow(taxa.I))
ZC=as.matrix(rbind(Z0,Z1))
#To label rows and columns
label.row=rbind(as.matrix(Z[,1]),taxa.I)
label.col=t(taxa.I)
#update the zero block by the given Z matrix
position=t(as.matrix(match(taxa.Z.col,taxa.I,nomatch = 0)))
ZC[1:nrow(taxa.Z),position]=as.matrix(Z[-1,-1])
#habdler of parents do not have phenotype (colums of Z are not in taxa.I)
# To do list
#To form final Z matrix
dataPart=rbind(label.col,ZC)
Z=data.frame(cbind(label.row,dataPart))
#print("GAPIT.ZmatrixFormation accomplished successfully!")
return(Z)
}#The function GAPIT.ZmatrixFormation ends here
#=============================================================================================
`GAPIT.cross_validation.compare` <-function(myGD=NULL,y=NULL, rel=NULL,tc=NULL){
# Object: GAPIT.cross validation compare to different folders by replicate Times,result:a pdf of the scree barplot and .cvs
# myGD:numeric SNP
# Y: phenotype with columns of taxa,Y1,Y2...
# rel:replications
# tc:comparation folds number and value
# Authors: You Tang,Jiabo Wang and You Zhou
# Last update: December 31, 2014
##############################################################################################
if(is.null(myGD)||is.null(y)){stop("Validation Invalid. Please select read valid flies !")}
if(is.null(rel))
{
rel=10 #not input rel value,default replications number is 10
}
if(rel<2){stop("Validation Invalid. Please select replications >1 !")}
#rel<-2 ##replications
#t<-2
y<-y[!is.na(y[,2]),]
y<-y[,c(1,2)]
y<- na.omit(y)
#############
commonGeno <- unique(as.character(y[,1]))[unique(as.character(y[,1])) %in% myGD[,1]]
cG<-data.frame(commonGeno)
names(cG)<-"Taxa"
colnames(y)<-c("Taxa","pheno")
y2<-merge(y,cG,all.x=FALSE, all.y=TRUE, by = c("Taxa"))
Z1 <- myGD[match(y2$Taxa,myGD[,1]),]
myGD<- Z1
y<-y2
##############
X<-myGD[,-1]
k1<-as.matrix(X)
k2=GAPIT.kinship.VanRaden(snps=k1)
myKI<-as.data.frame(k2)
myKI<-cbind(myGD[,1],myKI)
write.table(y,"Y.txt",quote=F,sep="\t",row.names=F,col.names=T)
write.table(myKI,"K.txt",quote=F,row.names=F,col.names=F,sep="\t")
gc()
myK<- read.table("K.txt",head=F)
y= read.table("Y.txt",head=T)
y<- na.omit(y)
y=y[(y[,1] %in% myK[,1]),]
m=nrow(y)
if(is.null(tc))
tc<-c(2,5,10,20,50) ##default compare to folders num
tc1<-as.matrix(tc)
allstorage.ref=matrix(0,rel,nrow(tc1))
allstorage.inf=matrix(0,rel,nrow(tc1))
for(w in 1:nrow(tc1)){
num<-tc1[w,]
m.sample=floor(m/num)
storage.ref=matrix(0,rel,num)
storage.inf=matrix(0,rel,num)
#storage.REML=matrix(0,rel,num)
for(k in 1:rel)
{
#################Rand group method 1############
sets=sample(cut(1:nrow(y),num,labels=FALSE),nrow(y))
sets = as.data.frame(sets)
ynew <- cbind(sets,y)
#i=sample(1:num, size = 1)
for(i in 1:num){
#use only genotypes that were genotyped and phenotyped
ref <- y$Taxa[!ynew$sets==i]
lines.cali<- ref
# ycali<- y[match(ref,y$Taxa),]
#use only genotypes that were genotyped and phenotyped
test <- y$Taxa[ynew$sets==i]
lines.vali<-test
#yvali<- y[match(test,y$Taxa),]
#################end Rand group method############
#use only genotypes that were genotyped and phenotyped
commonGeno_v <- lines.vali[lines.vali %in% myK[,1]]
yvali<- y[match(commonGeno_v,y[,1]),]
#use only genotypes that were genotyped and phenotyped
commonGeno_c <- lines.cali[lines.cali %in% myK[,1]]
ycali<- y[match(commonGeno_c,y[,1]),]
Y.raw=ycali[,c(1,2)]#choos a trait
myY=Y.raw
myKI=myK
max.groups=m
#Run GAPIT
#############################################
myGAPIT <- GAPIT(
Y=myY,
KI=myKI,
#group.from=max.groups,
group.from=max.groups,
group.to=max.groups,
#group.by=10,
PCA.total=3,
SNP.test=FALSE,
file.output=FALSE
)
prediction=myGAPIT$Pred
prediction.ref<-prediction[match(commonGeno_c,prediction$Taxa),]
prediction.inf<-prediction[match(commonGeno_v,prediction$Taxa),]
YP.ref <- merge(y, prediction.ref, by.x = 1, by.y = "Taxa")
YP.inf <- merge(y, prediction.inf, by.x = 1, by.y = "Taxa")
#Calculate correlation and store them
r.ref=cor(as.numeric(as.vector(YP.ref[,2])),as.numeric(as.vector(YP.ref[,6]) ))
r.inf=cor(as.numeric(as.vector(YP.inf[,2])),as.numeric(as.vector(YP.inf[,6]) ))
if(r.inf<0){
#r.inf=cor(as.numeric(as.vector(YP.inf[,2])),as.numeric(as.vector(YP.inf[,2]+YP.inf[,6])))
combine_output=cbind(as.numeric(as.vector(YP.inf[,2])),as.numeric(as.vector(YP.inf[,6]) ))
write.csv(combine_output, paste("Accuracy_folders",num,k,i,rel,".csv",sep=""))
#stop("...........")
}
storage.ref[k,i]=r.ref
storage.inf[k,i]=r.inf
print(paste(" rel= ", rel, " k= ",k," i= ",i,sep = ""))
}
print(paste("finish replications k= ",k," folders= ",num,sep = ""))
}
#Find missing position-->0.0
index=is.na(storage.inf)
storage.inf[index]=0
allstorage.inf[,w]=as.matrix(rowMeans(storage.inf))
allstorage.ref[,w]=as.matrix(rowMeans(storage.ref))
#as.matrix(rowMeans(storage.ref))
##output rel times and accuracy for every folders
combine_output=cbind(storage.inf,allstorage.inf[,w])
combine_output1=cbind(storage.ref,allstorage.ref[,w])
colnames(combine_output)=c(paste("folders",c(1:num),sep=""),"mean")
write.csv(combine_output, paste("Accuracy_folders",num,"by CMLM,rel_",rel,".csv",sep=""))
write.csv(combine_output1, paste("Accuracy_folders ref",num,"by CMLM,rel_",rel,".csv",sep=""))
}
sr<-nrow(tc1)
##output means accuracy by rel for every folders
colnames(allstorage.inf)=c(paste(tc1[c(1:sr),]," folders",sep=""))
write.csv(allstorage.inf, paste("Accuracy_folders",nrow(tc1),"by CMLM,rel_",rel,".compare to means",".csv",sep=""))
write.csv(allstorage.ref, paste("Accuracy_folders ref",nrow(tc1),"by CMLM,rel_",rel,".compare to means",".csv",sep=""))
name.of.trait=noquote(names(Y.raw)[2])
#rrel=round(rel/2)
#ppp<-matrix(0,sr,2)
ppp<-matrix(0,sr,2)
#if(rrel!=1){
# aarm<-colMeans(allstorage.inf[1:rrel,])
# }else{
# aarm<-allstorage.inf[1,]
# }
#aam<-colMeans(allstorage.inf)
aam<-allstorage.inf
aam<-data.frame(aam)
bbm<-allstorage.ref
bbm<-data.frame(bbm)
for(b in 1:sr){
#ppp[b,]<-as.matrix(c(aarm[b],aam[b]))
ppp[b,1]<-as.matrix(mean(aam[,b]))
#colnames(ppp)<-c(rrel,rel)
}
for(c in 1:sr){
ppp[c,2]<-as.matrix(mean(bbm[,c]))
}
ppp<-as.matrix(cbind(ppp,tc1))
#colnames(ppp)<-c(rel)
sj<-runif(1, 0, 1)
#name.of.trait="qqq"
pdf(paste("GAPIT.cross_validation ", name.of.trait,sj,".compare to different folders.", ".pdf", sep = ""),width = 4.5, height = 4,pointsize=9)
par(mar = c(5,6,5,3))
palette(c("blue","red",rainbow(2)))
plot(ppp[,3],ppp[,2],xaxt="n",ylim=c(0,1.04),xlim=c(min(tc1)-1,max(tc1)+1),bg="lightgray",xlab="Number of folds",ylab="Correlation",type="o",pch=1,col=1,cex=1.0,cex.lab=1.7, cex.axis=1.3, lwd=3,las=1,lty =2)
axis(side=1,at=tc1,labels=tc1,cex.lab=1.7)
lines(ppp[,1]~ppp[,3], lwd=3,type="o",pch=19,col=2,lty =1)
legend("bottomright",horiz = FALSE,c("Reference","Inference"),pch = c(1,19), lty =c(2,1),col=c(1:2),lwd=2,cex=1.2,bty="n")
dev.off()
print(paste("GAPIT.cross validation ", name.of.trait,".compare to different folders.","successfully!" ,sep = ""))
return(list(allstorage.inf))
}#end GAPIT.cross validation compare to different folders by replicate Times
#=============================================================================================
emma.kinship <- function(snps, method="additive", use="all") {
n0 <- sum(snps==0,na.rm=TRUE)
nh <- sum(snps==0.5,na.rm=TRUE)
n1 <- sum(snps==1,na.rm=TRUE)
nNA <- sum(is.na(snps))
stopifnot(n0+nh+n1+nNA == length(snps))
if ( method == "dominant" ) {
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) > 0.5),nrow(snps),ncol(snps))
snps[!is.na(snps) && (snps == 0.5)] <- flags[!is.na(snps) && (snps == 0.5)]
}
else if ( method == "recessive" ) {
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) < 0.5),nrow(snps),ncol(snps))
snps[!is.na(snps) && (snps == 0.5)] <- flags[!is.na(snps) && (snps == 0.5)]
}
else if ( ( method == "additive" ) && ( nh > 0 ) ) {
dsnps <- snps
rsnps <- snps
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) > 0.5),nrow(snps),ncol(snps))
dsnps[!is.na(snps) && (snps==0.5)] <- flags[is.na(snps) && (snps==0.5)]
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) < 0.5),nrow(snps),ncol(snps))
rsnps[!is.na(snps) && (snps==0.5)] <- flags[is.na(snps) && (snps==0.5)]
snps <- rbind(dsnps,rsnps)
}
if ( use == "all" ) {
mafs <- matrix(rowMeans(snps,na.rm=TRUE),nrow(snps),ncol(snps))
snps[is.na(snps)] <- mafs[is.na(snps)]
}
else if ( use == "complete.obs" ) {
snps <- snps[rowSums(is.na(snps))==0,]
}
n <- ncol(snps)
K <- matrix(nrow=n,ncol=n)
diag(K) <- 1
for(i in 1:(n-1)) {
for(j in (i+1):n) {
x <- snps[,i]*snps[,j] + (1-snps[,i])*(1-snps[,j])
K[i,j] <- sum(x,na.rm=TRUE)/sum(!is.na(x))
K[j,i] <- K[i,j]
}
}
return(K)
}
emma.eigen.L <- function(Z,K,complete=TRUE) {
if ( is.null(Z) ) {
return(emma.eigen.L.wo.Z(K))
}
else {
return(emma.eigen.L.w.Z(Z,K,complete))
}
}
emma.eigen.L.wo.Z <- function(K) {
eig <- eigen(K,symmetric=TRUE)
return(list(values=eig$values,vectors=eig$vectors))
}
emma.eigen.L.w.Z <- function(Z,K,complete=TRUE) {
if ( complete == FALSE ) {
vids <- colSums(Z)>0
Z <- Z[,vids]
K <- K[vids,vids]
}
eig <- eigen(K%*%crossprod(Z,Z),symmetric=FALSE,EISPACK=TRUE)
return(list(values=eig$values,vectors=qr.Q(qr(Z%*%eig$vectors),complete=TRUE)))
}
emma.eigen.R <- function(Z,K,X,complete=TRUE) {
if ( is.null(Z) ) {
return(emma.eigen.R.wo.Z(K,X))
}
else {
return(emma.eigen.R.w.Z(Z,K,X,complete))
}
}
emma.eigen.R.wo.Z <- function(K, X) {
n <- nrow(X)
q <- ncol(X)
S <- diag(n)-X%*%solve(crossprod(X,X))%*%t(X)
eig <- eigen(S%*%(K+diag(1,n))%*%S,symmetric=TRUE)
stopifnot(!is.complex(eig$values))
return(list(values=eig$values[1:(n-q)]-1,vectors=eig$vectors[,1:(n-q)]))
}
emma.eigen.R.w.Z <- function(Z, K, X, complete = TRUE) {
if ( complete == FALSE ) {
vids <- colSums(Z) > 0
Z <- Z[,vids]
K <- K[vids,vids]
}
n <- nrow(Z)
t <- ncol(Z)
q <- ncol(X)
SZ <- Z - X%*%solve(crossprod(X,X))%*%crossprod(X,Z)
eig <- eigen(K%*%crossprod(Z,SZ),symmetric=FALSE,EISPACK=TRUE)
if ( is.complex(eig$values) ) {
eig$values <- Re(eig$values)
eig$vectors <- Re(eig$vectors)
}
qr.X <- qr.Q(qr(X))
return(list(values=eig$values[1:(t-q)],
vectors=qr.Q(qr(cbind(SZ%*%eig$vectors[,1:(t-q)],qr.X)),
complete=TRUE)[,c(1:(t-q),(t+1):n)]))
}
emma.delta.ML.LL.wo.Z <- function(logdelta, lambda, etas, xi) {
n <- length(xi)
delta <- exp(logdelta)
return( 0.5*(n*(log(n/(2*pi))-1-log(sum((etas*etas)/(lambda+delta))))-sum(log(xi+delta))) )
}
emma.delta.ML.LL.w.Z <- function(logdelta, lambda, etas.1, xi.1, n, etas.2.sq ) {
t <- length(xi.1)
delta <- exp(logdelta)
# stopifnot(length(lambda) == length(etas.1))
return( 0.5*(n*(log(n/(2*pi))-1-log(sum(etas.1*etas.1/(lambda+delta))+etas.2.sq/delta))-(sum(log(xi.1+delta))+(n-t)*logdelta)) )
}
emma.delta.ML.dLL.wo.Z <- function(logdelta, lambda, etas, xi) {
n <- length(xi)
delta <- exp(logdelta)
etasq <- etas*etas
ldelta <- lambda+delta
return( 0.5*(n*sum(etasq/(ldelta*ldelta))/sum(etasq/ldelta)-sum(1/(xi+delta))) )
}
emma.delta.ML.dLL.w.Z <- function(logdelta, lambda, etas.1, xi.1, n, etas.2.sq ) {
t <- length(xi.1)
q <- t-length(lambda)
delta <- exp(logdelta)
etasq <- etas.1*etas.1
ldelta <- lambda+delta
return( 0.5*(n*(sum(etasq/(ldelta*ldelta))+etas.2.sq/(delta*delta))/(sum(etasq/ldelta)+etas.2.sq/delta)-(sum(1/(xi.1+delta))+(n-t)/delta) ) )
}
emma.delta.REML.LL.wo.Z <- function(logdelta, lambda, etas) {
nq <- length(etas)
delta <- exp(logdelta)
return( 0.5*(nq*(log(nq/(2*pi))-1-log(sum(etas*etas/(lambda+delta))))-sum(log(lambda+delta))) )
}
emma.delta.REML.LL.w.Z <- function(logdelta, lambda, etas.1, n, t, etas.2.sq ) {
tq <- length(etas.1)
nq <- n - t + tq
delta <- exp(logdelta)
return( 0.5*(nq*(log(nq/(2*pi))-1-log(sum(etas.1*etas.1/(lambda+delta))+etas.2.sq/delta))-(sum(log(lambda+delta))+(n-t)*logdelta)) )
}
emma.delta.REML.dLL.wo.Z <- function(logdelta, lambda, etas) {
nq <- length(etas)
delta <- exp(logdelta)
etasq <- etas*etas
ldelta <- lambda+delta
return( 0.5*(nq*sum(etasq/(ldelta*ldelta))/sum(etasq/ldelta)-sum(1/ldelta)) )
}
emma.delta.REML.dLL.w.Z <- function(logdelta, lambda, etas.1, n, t1, etas.2.sq ) {
t <- t1
tq <- length(etas.1)
nq <- n - t + tq
delta <- exp(logdelta)
etasq <- etas.1*etas.1
ldelta <- lambda+delta
return( 0.5*(nq*(sum(etasq/(ldelta*ldelta))+etas.2.sq/(delta*delta))/(sum(etasq/ldelta)+etas.2.sq/delta)-(sum(1/ldelta)+(n-t)/delta)) )
}
emma.MLE <- function(y, X, K, Z=NULL, ngrids=100, llim=-10, ulim=10,
esp=1e-10, eig.L = NULL, eig.R = NULL)
{
n <- length(y)
t <- nrow(K)
q <- ncol(X)
# stopifnot(nrow(K) == t)
stopifnot(ncol(K) == t)
stopifnot(nrow(X) == n)
if ( det(crossprod(X,X)) == 0 ) {
warning("X is singular")
return (list(ML=0,delta=0,ve=0,vg=0))
}
if ( is.null(Z) ) {
if ( is.null(eig.L) ) {
eig.L <- emma.eigen.L.wo.Z(K)
}
if ( is.null(eig.R) ) {
eig.R <- emma.eigen.R.wo.Z(K,X)
}
etas <- crossprod(eig.R$vectors,y)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,n-q,m) + matrix(delta,n-q,m,byrow=TRUE)
Xis <- matrix(eig.L$values,n,m) + matrix(delta,n,m,byrow=TRUE)
Etasq <- matrix(etas*etas,n-q,m)
LL <- 0.5*(n*(log(n/(2*pi))-1-log(colSums(Etasq/Lambdas)))-colSums(log(Xis)))
dLL <- 0.5*delta*(n*colSums(Etasq/(Lambdas*Lambdas))/colSums(Etasq/Lambdas)-colSums(1/Xis))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if ( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.ML.LL.wo.Z(llim,eig.R$values,etas,eig.L$values))
}
if ( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.ML.LL.wo.Z(ulim,eig.R$values,etas,eig.L$values))
}
for( i in 1:(m-1) )
{
if ( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.ML.dLL.wo.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas=etas, xi=eig.L$values)
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.ML.LL.wo.Z(r$root,eig.R$values, etas, eig.L$values))
}
}
# optdelta <- exp(optlogdelta)
}
else {
if ( is.null(eig.L) ) {
eig.L <- emma.eigen.L.w.Z(Z,K)
}
if ( is.null(eig.R) ) {
eig.R <- emma.eigen.R.w.Z(Z,K,X)
}
etas <- crossprod(eig.R$vectors,y)
etas.1 <- etas[1:(t-q)]
etas.2 <- etas[(t-q+1):(n-q)]
etas.2.sq <- sum(etas.2*etas.2)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,t-q,m) + matrix(delta,t-q,m,byrow=TRUE)
Xis <- matrix(eig.L$values,t,m) + matrix(delta,t,m,byrow=TRUE)
Etasq <- matrix(etas.1*etas.1,t-q,m)
#LL <- 0.5*(n*(log(n/(2*pi))-1-log(colSums(Etasq/Lambdas)+etas.2.sq/delta))-colSums(log(Xis))+(n-t)*log(deltas))
dLL <- 0.5*delta*(n*(colSums(Etasq/(Lambdas*Lambdas))+etas.2.sq/(delta*delta))/(colSums(Etasq/Lambdas)+etas.2.sq/delta)-(colSums(1/Xis)+(n-t)/delta))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if ( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.ML.LL.w.Z(llim,eig.R$values,etas.1,eig.L$values,n,etas.2.sq))
}
if ( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.ML.LL.w.Z(ulim,eig.R$values,etas.1,eig.L$values,n,etas.2.sq))
}
for( i in 1:(m-1) )
{
if ( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.ML.dLL.w.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas.1=etas.1, xi.1=eig.L$values, n=n, etas.2.sq = etas.2.sq )
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.ML.LL.w.Z(r$root,eig.R$values, etas.1, eig.L$values, n, etas.2.sq ))
}
}
# optdelta <- exp(optlogdelta)
}
maxdelta <- exp(optlogdelta[which.max(optLL)])
maxLL <- max(optLL)
if ( is.null(Z) ) {
maxva <- sum(etas*etas/(eig.R$values+maxdelta))/n
}
else {
maxva <- (sum(etas.1*etas.1/(eig.R$values+maxdelta))+etas.2.sq/maxdelta)/n
}
maxve <- maxva*maxdelta
return (list(ML=maxLL,delta=maxdelta,ve=maxve,vg=maxva))
}
emma.REMLE <- function(y, X, K, Z=NULL, ngrids=100, llim=-10, ulim=10,
esp=1e-10, eig.L = NULL, eig.R = NULL) {
n <- length(y)
t <- nrow(K)
q <- ncol(X)
# stopifnot(nrow(K) == t)
stopifnot(ncol(K) == t)
stopifnot(nrow(X) == n)
if ( det(crossprod(X,X)) == 0 ) {
warning("X is singular")
return (list(REML=0,delta=0,ve=0,vg=0))
}
if ( is.null(Z) ) {
if ( is.null(eig.R) ) {
eig.R <- emma.eigen.R.wo.Z(K,X)
}
etas <- crossprod(eig.R$vectors,y)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,n-q,m) + matrix(delta,n-q,m,byrow=TRUE)
Etasq <- matrix(etas*etas,n-q,m)
LL <- 0.5*((n-q)*(log((n-q)/(2*pi))-1-log(colSums(Etasq/Lambdas)))-colSums(log(Lambdas)))
dLL <- 0.5*delta*((n-q)*colSums(Etasq/(Lambdas*Lambdas))/colSums(Etasq/Lambdas)-colSums(1/Lambdas))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if ( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(llim,eig.R$values,etas))
}
if ( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(ulim,eig.R$values,etas))
}
for( i in 1:(m-1) )
{
if ( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.REML.dLL.wo.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas=etas)
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(r$root,eig.R$values, etas))
}
}
# optdelta <- exp(optlogdelta)
}
else {
if ( is.null(eig.R) ) {
eig.R <- emma.eigen.R.w.Z(Z,K,X)
}
etas <- crossprod(eig.R$vectors,y)
etas.1 <- etas[1:(t-q)]
etas.2 <- etas[(t-q+1):(n-q)]
etas.2.sq <- sum(etas.2*etas.2)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,t-q,m) + matrix(delta,t-q,m,byrow=TRUE)
Etasq <- matrix(etas.1*etas.1,t-q,m)
dLL <- 0.5*delta*((n-q)*(colSums(Etasq/(Lambdas*Lambdas))+etas.2.sq/(delta*delta))/(colSums(Etasq/Lambdas)+etas.2.sq/delta)-(colSums(1/Lambdas)+(n-t)/delta))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if ( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(llim,eig.R$values,etas.1,n,t,etas.2.sq))
}
if ( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(ulim,eig.R$values,etas.1,n,t,etas.2.sq))
}
for( i in 1:(m-1) )
{
if ( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.REML.dLL.w.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas.1=etas.1, n=n, t1=t, etas.2.sq = etas.2.sq )
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(r$root,eig.R$values, etas.1, n, t, etas.2.sq ))
}
}
# optdelta <- exp(optlogdelta)
}
maxdelta <- exp(optlogdelta[which.max(optLL)])
maxLL <- max(optLL)
if ( is.null(Z) ) {
maxva <- sum(etas*etas/(eig.R$values+maxdelta))/(n-q)
}
else {
maxva <- (sum(etas.1*etas.1/(eig.R$values+maxdelta))+etas.2.sq/maxdelta)/(n-q)
}
maxve <- maxva*maxdelta
return (list(REML=maxLL,delta=maxdelta,ve=maxve,vg=maxva))
}
emma.ML.LRT <- function(ys, xs, K, Z=NULL, X0 = NULL, ngrids=100, llim=-10, ulim=10, esp=1e-10, ponly = FALSE) {
if ( is.null(dim(ys)) || ncol(ys) == 1 ) {
ys <- matrix(ys,1,length(ys))
}
if ( is.null(dim(xs)) || ncol(xs) == 1 ) {
xs <- matrix(xs,1,length(xs))
}
if ( is.null(X0) ) {
X0 <- matrix(1,ncol(ys),1)
}
g <- nrow(ys)
n <- ncol(ys)
m <- nrow(xs)
t <- ncol(xs)
q0 <- ncol(X0)
q1 <- q0 + 1
if ( !ponly ) {
ML1s <- matrix(nrow=m,ncol=g)
ML0s <- matrix(nrow=m,ncol=g)
vgs <- matrix(nrow=m,ncol=g)
ves <- matrix(nrow=m,ncol=g)
}
stats <- matrix(nrow=m,ncol=g)
ps <- matrix(nrow=m,ncol=g)
ML0 <- vector(length=g)
stopifnot(nrow(K) == t)
stopifnot(ncol(K) == t)
stopifnot(nrow(X0) == n)
if ( sum(is.na(ys)) == 0 ) {
eig.L <- emma.eigen.L(Z,K)
eig.R0 <- emma.eigen.R(Z,K,X0)
for(i in 1:g) {
ML0[i] <- emma.MLE(ys[i,],X0,K,Z,ngrids,llim,ulim,esp,eig.L,eig.R0)$ML
}
x.prev <- vector(length=0)
for(i in 1:m) {
vids <- !is.na(xs[i,])
nv <- sum(vids)
xv <- xs[i,vids]
if ( ( mean(xv) <= 0 ) || ( mean(xv) >= 1 ) ) {
if (!ponly) {
stats[i,] <- rep(NA,g)
vgs[i,] <- rep(NA,g)
ves[i,] <- rep(NA,g)
ML1s[i,] <- rep(NA,g)
ML0s[i,] <- rep(NA,g)
}
ps[i,] = rep(1,g)
}
else if ( identical(x.prev, xv) ) {
if ( !ponly ) {
stats[i,] <- stats[i-1,]
vgs[i,] <- vgs[i-1,]
ves[i,] <- ves[i-1,]
ML1s[i,] <- ML1s[i-1,]
ML0s[i,] <- ML0s[i-1,]
}
ps[i,] <- ps[i-1,]
}
else {
if ( is.null(Z) ) {
X <- cbind(X0[vids,,drop=FALSE],xs[i,vids])
eig.R1 = emma.eigen.R.wo.Z(K[vids,vids],X)
}
else {
vrows <- as.logical(rowSums(Z[,vids]))
nr <- sum(vrows)
X <- cbind(X0[vrows,,drop=FALSE],Z[vrows,vids]%*%t(xs[i,vids,drop=FALSE]))
eig.R1 = emma.eigen.R.w.Z(Z[vrows,vids],K[vids,vids],X)
}
for(j in 1:g) {
if ( nv == t ) {
MLE <- emma.MLE(ys[j,],X,K,Z,ngrids,llim,ulim,esp,eig.L,eig.R1)
# MLE <- emma.MLE(ys[j,],X,K,Z,ngrids,llim,ulim,esp,eig.L,eig.R1)
if (!ponly) {
ML1s[i,j] <- MLE$ML
vgs[i,j] <- MLE$vg
ves[i,j] <- MLE$ve
}
stats[i,j] <- 2*(MLE$ML-ML0[j])
}
else {
if ( is.null(Z) ) {
eig.L0 <- emma.eigen.L.wo.Z(K[vids,vids])
MLE0 <- emma.MLE(ys[j,vids],X0[vids,,drop=FALSE],K[vids,vids],NULL,ngrids,llim,ulim,esp,eig.L0)
MLE1 <- emma.MLE(ys[j,vids],X,K[vids,vids],NULL,ngrids,llim,ulim,esp,eig.L0)
}
else {
if ( nr == n ) {
MLE1 <- emma.MLE(ys[j,],X,K,Z,ngrids,llim,ulim,esp,eig.L)
}
else {
eig.L0 <- emma.eigen.L.w.Z(Z[vrows,vids],K[vids,vids])
MLE0 <- emma.MLE(ys[j,vrows],X0[vrows,,drop=FALSE],K[vids,vids],Z[vrows,vids],ngrids,llim,ulim,esp,eig.L0)
MLE1 <- emma.MLE(ys[j,vrows],X,K[vids,vids],Z[vrows,vids],ngrids,llim,ulim,esp,eig.L0)
}
}
if (!ponly) {
ML1s[i,j] <- MLE1$ML
ML0s[i,j] <- MLE0$ML
vgs[i,j] <- MLE1$vg
ves[i,j] <- MLE1$ve
}
stats[i,j] <- 2*(MLE1$ML-MLE0$ML)
}
}
if ( ( nv == t ) && ( !ponly ) ) {
ML0s[i,] <- ML0
}
ps[i,] <- pchisq(stats[i,],1,lower.tail=FALSE)
}
}
}
else {
eig.L <- emma.eigen.L(Z,K)
eig.R0 <- emma.eigen.R(Z,K,X0)
for(i in 1:g) {
vrows <- !is.na(ys[i,])
if ( is.null(Z) ) {
ML0[i] <- emma.MLE(ys[i,vrows],X0[vrows,,drop=FALSE],K[vrows,vrows],NULL,ngrids,llim,ulim,esp)$ML
}
else {
vids <- colSums(Z[vrows,]>0)
ML0[i] <- emma.MLE(ys[i,vrows],X0[vrows,,drop=FALSE],K[vids,vids],Z[vrows,vids],ngrids,llim,ulim,esp)$ML
}
}
x.prev <- vector(length=0)
for(i in 1:m) {
vids <- !is.na(xs[i,])
nv <- sum(vids)
xv <- xs[i,vids]
if ( ( mean(xv) <= 0 ) || ( mean(xv) >= 1 ) ) {
if (!ponly) {
stats[i,] <- rep(NA,g)
vgs[i,] <- rep(NA,g)
ves[i,] <- rep(NA,g)
ML1s[i,] <- rep(NA,g)
ML0s[,i] <- rep(NA,g)
}
ps[i,] = rep(1,g)
}
else if ( identical(x.prev, xv) ) {
if ( !ponly ) {
stats[i,] <- stats[i-1,]
vgs[i,] <- vgs[i-1,]
ves[i,] <- ves[i-1,]
ML1s[i,] <- ML1s[i-1,]
}
ps[i,] = ps[i-1,]
}
else {
if ( is.null(Z) ) {
X <- cbind(X0,xs[i,])
if ( nv == t ) {
eig.R1 = emma.eigen.R.wo.Z(K,X)
}
}
else {
vrows <- as.logical(rowSums(Z[,vids]))
X <- cbind(X0,Z[,vids,drop=FALSE]%*%t(xs[i,vids,drop=FALSE]))
if ( nv == t ) {
eig.R1 = emma.eigen.R.w.Z(Z,K,X)
}
}
for(j in 1:g) {
# print(j)
vrows <- !is.na(ys[j,])
if ( nv == t ) {
nr <- sum(vrows)
if ( is.null(Z) ) {
if ( nr == n ) {
MLE <- emma.MLE(ys[j,],X,K,NULL,ngrids,llim,ulim,esp,eig.L,eig.R1)
}
else {
MLE <- emma.MLE(ys[j,vrows],X[vrows,],K[vrows,vrows],NULL,ngrids,llim,ulim,esp)
}
}
else {
if ( nr == n ) {
MLE <- emma.MLE(ys[j,],X,K,Z,ngrids,llim,ulim,esp,eig.L,eig.R1)
}
else {
vtids <- as.logical(colSums(Z[vrows,,drop=FALSE]))
MLE <- emma.MLE(ys[j,vrows],X[vrows,],K[vtids,vtids],Z[vrows,vtids],ngrids,llim,ulim,esp)
}
}
if (!ponly) {
ML1s[i,j] <- MLE$ML
vgs[i,j] <- MLE$vg
ves[i,j] <- MLE$ve
}
stats[i,j] <- 2*(MLE$ML-ML0[j])
}
else {
if ( is.null(Z) ) {
vtids <- vrows & vids
eig.L0 <- emma.eigen.L(NULL,K[vtids,vtids])
MLE0 <- emma.MLE(ys[j,vtids],X0[vtids,,drop=FALSE],K[vtids,vtids],NULL,ngrids,llim,ulim,esp,eig.L0)
MLE1 <- emma.MLE(ys[j,vtids],X[vtids,],K[vtids,vtids],NULL,ngrids,llim,ulim,esp,eig.L0)
}
else {
vtids <- as.logical(colSums(Z[vrows,])) & vids
vtrows <- vrows & as.logical(rowSums(Z[,vids]))
eig.L0 <- emma.eigen.L(Z[vtrows,vtids],K[vtids,vtids])
MLE0 <- emma.MLE(ys[j,vtrows],X0[vtrows,,drop=FALSE],K[vtids,vtids],Z[vtrows,vtids],ngrids,llim,ulim,esp,eig.L0)
MLE1 <- emma.MLE(ys[j,vtrows],X[vtrows,],K[vtids,vtids],Z[vtrows,vtids],ngrids,llim,ulim,esp,eig.L0)
}
if (!ponly) {
ML1s[i,j] <- MLE1$ML
vgs[i,j] <- MLE1$vg
ves[i,j] <- MLE1$ve
ML0s[i,j] <- MLE0$ML
}
stats[i,j] <- 2*(MLE1$ML-MLE0$ML)
}
}
if ( ( nv == t ) && ( !ponly ) ) {
ML0s[i,] <- ML0
}
ps[i,] <- pchisq(stats[i,],1,lower.tail=FALSE)
}
}
}
if ( ponly ) {
return (ps)
}
else {
return (list(ps=ps,ML1s=ML1s,ML0s=ML0s,stats=stats,vgs=vgs,ves=ves))
}
}
emma.REML.t <- function(ys, xs, K, Z=NULL, X0 = NULL, ngrids=100, llim=-10, ulim=10, esp=1e-10, ponly = FALSE) {
if ( is.null(dim(ys)) || ncol(ys) == 1 ) {
ys <- matrix(ys,1,length(ys))
}
if ( is.null(dim(xs)) || ncol(xs) == 1 ) {
xs <- matrix(xs,1,length(xs))
}
if ( is.null(X0) ) {
X0 <- matrix(1,ncol(ys),1)
}
g <- nrow(ys)
n <- ncol(ys)
m <- nrow(xs)
t <- ncol(xs)
q0 <- ncol(X0)
q1 <- q0 + 1
stopifnot(nrow(K) == t)
stopifnot(ncol(K) == t)
stopifnot(nrow(X0) == n)
if ( !ponly ) {
REMLs <- matrix(nrow=m,ncol=g)
vgs <- matrix(nrow=m,ncol=g)
ves <- matrix(nrow=m,ncol=g)
}
dfs <- matrix(nrow=m,ncol=g)
stats <- matrix(nrow=m,ncol=g)
ps <- matrix(nrow=m,ncol=g)
if ( sum(is.na(ys)) == 0 ) {
eig.L <- emma.eigen.L(Z,K)
x.prev <- vector(length=0)
for(i in 1:m) {
vids <- !is.na(xs[i,])
nv <- sum(vids)
xv <- xs[i,vids]
if ( ( mean(xv) <= 0 ) || ( mean(xv) >= 1 ) ) {
if ( !ponly ) {
vgs[i,] <- rep(NA,g)
ves[i,] <- rep(NA,g)
dfs[i,] <- rep(NA,g)
REMLs[i,] <- rep(NA,g)
stats[i,] <- rep(NA,g)
}
ps[i,] = rep(1,g)
}
else if ( identical(x.prev, xv) ) {
if ( !ponly ) {
vgs[i,] <- vgs[i-1,]
ves[i,] <- ves[i-1,]
dfs[i,] <- dfs[i-1,]
REMLs[i,] <- REMLs[i-1,]
stats[i,] <- stats[i-1,]
}
ps[i,] <- ps[i-1,]
}
else {
if ( is.null(Z) ) {
X <- cbind(X0[vids,,drop=FALSE],xs[i,vids])
eig.R1 = emma.eigen.R.wo.Z(K[vids,vids],X)
}
else {
vrows <- as.logical(rowSums(Z[,vids]))
X <- cbind(X0[vrows,,drop=FALSE],Z[vrows,vids,drop=FALSE]%*%t(xs[i,vids,drop=FALSE]))
eig.R1 = emma.eigen.R.w.Z(Z[vrows,vids],K[vids,vids],X)
}
for(j in 1:g) {
if ( nv == t ) {
REMLE <- emma.REMLE(ys[j,],X,K,Z,ngrids,llim,ulim,esp,eig.R1)
if ( is.null(Z) ) {
U <- eig.L$vectors * matrix(sqrt(1/(eig.L$values+REMLE$delta)),t,t,byrow=TRUE)
dfs[i,j] <- nv - q1
}
else {
U <- eig.L$vectors * matrix(c(sqrt(1/(eig.L$values+REMLE$delta)),rep(sqrt(1/REMLE$delta),n-t)),n,n,byrow=TRUE)
dfs[i,j] <- n - q1
}
yt <- crossprod(U,ys[j,])
Xt <- crossprod(U,X)
iXX <- solve(crossprod(Xt,Xt))
beta <- iXX%*%crossprod(Xt,yt)
if ( !ponly ) {
vgs[i,j] <- REMLE$vg
ves[i,j] <- REMLE$ve
REMLs[i,j] <- REMLE$REML
}
stats[i,j] <- beta[q1]/sqrt(iXX[q1,q1]*REMLE$vg)
}
else {
if ( is.null(Z) ) {
eig.L0 <- emma.eigen.L.wo.Z(K[vids,vids])
nr <- sum(vids)
yv <- ys[j,vids]
REMLE <- emma.REMLE(yv,X,K[vids,vids,drop=FALSE],NULL,ngrids,llim,ulim,esp,eig.R1)
U <- eig.L0$vectors * matrix(sqrt(1/(eig.L0$values+REMLE$delta)),nr,nr,byrow=TRUE)
dfs[i,j] <- nr - q1
}
else {
eig.L0 <- emma.eigen.L.w.Z(Z[vrows,vids,drop=FALSE],K[vids,vids])
yv <- ys[j,vrows]
nr <- sum(vrows)
tv <- sum(vids)
REMLE <- emma.REMLE(yv,X,K[vids,vids,drop=FALSE],Z[vrows,vids,drop=FALSE],ngrids,llim,ulim,esp,eig.R1)
U <- eig.L0$vectors * matrix(c(sqrt(1/(eig.L0$values+REMLE$delta)),rep(sqrt(1/REMLE$delta),nr-tv)),nr,nr,byrow=TRUE)
dfs[i,j] <- nr - q1
}
yt <- crossprod(U,yv)
Xt <- crossprod(U,X)
iXX <- solve(crossprod(Xt,Xt))
beta <- iXX%*%crossprod(Xt,yt)
if (!ponly) {
vgs[i,j] <- REMLE$vg
ves[i,j] <- REMLE$ve
REMLs[i,j] <- REMLE$REML
}
stats[i,j] <- beta[q1]/sqrt(iXX[q1,q1]*REMLE$vg)
}
}
ps[i,] <- 2*pt(abs(stats[i,]),dfs[i,],lower.tail=FALSE)
}
}
}
else {
eig.L <- emma.eigen.L(Z,K)
eig.R0 <- emma.eigen.R(Z,K,X0)
x.prev <- vector(length=0)
for(i in 1:m) {
vids <- !is.na(xs[i,])
nv <- sum(vids)
xv <- xs[i,vids]
if ( ( mean(xv) <= 0 ) || ( mean(xv) >= 1 ) ) {
if (!ponly) {
vgs[i,] <- rep(NA,g)
ves[i,] <- rep(NA,g)
REMLs[i,] <- rep(NA,g)
dfs[i,] <- rep(NA,g)
}
ps[i,] = rep(1,g)
}
else if ( identical(x.prev, xv) ) {
if ( !ponly ) {
stats[i,] <- stats[i-1,]
vgs[i,] <- vgs[i-1,]
ves[i,] <- ves[i-1,]
REMLs[i,] <- REMLs[i-1,]
dfs[i,] <- dfs[i-1,]
}
ps[i,] = ps[i-1,]
}
else {
if ( is.null(Z) ) {
X <- cbind(X0,xs[i,])
if ( nv == t ) {
eig.R1 = emma.eigen.R.wo.Z(K,X)
}
}
else {
vrows <- as.logical(rowSums(Z[,vids,drop=FALSE]))
X <- cbind(X0,Z[,vids,drop=FALSE]%*%t(xs[i,vids,drop=FALSE]))
if ( nv == t ) {
eig.R1 = emma.eigen.R.w.Z(Z,K,X)
}
}
for(j in 1:g) {
vrows <- !is.na(ys[j,])
if ( nv == t ) {
yv <- ys[j,vrows]
nr <- sum(vrows)
if ( is.null(Z) ) {
if ( nr == n ) {
REMLE <- emma.REMLE(yv,X,K,NULL,ngrids,llim,ulim,esp,eig.R1)
U <- eig.L$vectors * matrix(sqrt(1/(eig.L$values+REMLE$delta)),n,n,byrow=TRUE)
}
else {
eig.L0 <- emma.eigen.L.wo.Z(K[vrows,vrows,drop=FALSE])
REMLE <- emma.REMLE(yv,X[vrows,,drop=FALSE],K[vrows,vrows,drop=FALSE],NULL,ngrids,llim,ulim,esp)
U <- eig.L0$vectors * matrix(sqrt(1/(eig.L0$values+REMLE$delta)),nr,nr,byrow=TRUE)
}
dfs[i,j] <- nr-q1
}
else {
if ( nr == n ) {
REMLE <- emma.REMLE(yv,X,K,Z,ngrids,llim,ulim,esp,eig.R1)
U <- eig.L$vectors * matrix(c(sqrt(1/(eig.L$values+REMLE$delta)),rep(sqrt(1/REMLE$delta),n-t)),n,n,byrow=TRUE)
}
else {
vtids <- as.logical(colSums(Z[vrows,,drop=FALSE]))
eig.L0 <- emma.eigen.L.w.Z(Z[vrows,vtids,drop=FALSE],K[vtids,vtids,drop=FALSE])
REMLE <- emma.REMLE(yv,X[vrows,,drop=FALSE],K[vtids,vtids,drop=FALSE],Z[vrows,vtids,drop=FALSE],ngrids,llim,ulim,esp)
U <- eig.L0$vectors * matrix(c(sqrt(1/(eig.L0$values+REMLE$delta)),rep(sqrt(1/REMLE$delta),nr-sum(vtids))),nr,nr,byrow=TRUE)
}
dfs[i,j] <- nr-q1
}
yt <- crossprod(U,yv)
Xt <- crossprod(U,X[vrows,,drop=FALSE])
iXX <- solve(crossprod(Xt,Xt))
beta <- iXX%*%crossprod(Xt,yt)
if ( !ponly ) {
vgs[i,j] <- REMLE$vg
ves[i,j] <- REMLE$ve
REMLs[i,j] <- REMLE$REML
}
stats[i,j] <- beta[q1]/sqrt(iXX[q1,q1]*REMLE$vg)
}
else {
if ( is.null(Z) ) {
vtids <- vrows & vids
eig.L0 <- emma.eigen.L.wo.Z(K[vtids,vtids,drop=FALSE])
yv <- ys[j,vtids]
nr <- sum(vtids)
REMLE <- emma.REMLE(yv,X[vtids,,drop=FALSE],K[vtids,vtids,drop=FALSE],NULL,ngrids,llim,ulim,esp)
U <- eig.L0$vectors * matrix(sqrt(1/(eig.L0$values+REMLE$delta)),nr,nr,byrow=TRUE)
Xt <- crossprod(U,X[vtids,,drop=FALSE])
dfs[i,j] <- nr-q1
}
else {
vtids <- as.logical(colSums(Z[vrows,,drop=FALSE])) & vids
vtrows <- vrows & as.logical(rowSums(Z[,vids,drop=FALSE]))
eig.L0 <- emma.eigen.L.w.Z(Z[vtrows,vtids,drop=FALSE],K[vtids,vtids,drop=FALSE])
yv <- ys[j,vtrows]
nr <- sum(vtrows)
REMLE <- emma.REMLE(yv,X[vtrows,,drop=FALSE],K[vtids,vtids,drop=FALSE],Z[vtrows,vtids,drop=FALSE],ngrids,llim,ulim,esp)
U <- eig.L0$vectors * matrix(c(sqrt(1/(eig.L0$values+REMLE$delta)),rep(sqrt(1/REMLE$delta),nr-sum(vtids))),nr,nr,byrow=TRUE)
Xt <- crossprod(U,X[vtrows,,drop=FALSE])
dfs[i,j] <- nr-q1
}
yt <- crossprod(U,yv)
iXX <- solve(crossprod(Xt,Xt))
beta <- iXX%*%crossprod(Xt,yt)
if ( !ponly ) {
vgs[i,j] <- REMLE$vg
ves[i,j] <- REMLE$ve
REMLs[i,j] <- REMLE$REML
}
stats[i,j] <- beta[q1]/sqrt(iXX[q1,q1]*REMLE$vg)
}
}
ps[i,] <- 2*pt(abs(stats[i,]),dfs[i,],lower.tail=FALSE)
}
}
}
if ( ponly ) {
return (ps)
}
else {
return (list(ps=ps,REMLs=REMLs,stats=stats,dfs=dfs,vgs=vgs,ves=ves))
}
}
`GAPIT.emma.REMLE` <-
function(y, X, K, Z=NULL, ngrids=100, llim=-10, ulim=10,
esp=1e-10, eig.L = NULL, eig.R = NULL) {
# Authors: Hyun Min Kang
# Modified (only one line) by Zhiwu Zhang to handle non-defined LL ("NaN") by replacing it with the worst LL.
# Last update: June 8, 2011
##############################################################################################
n <- length(y)
t <- nrow(K)
q <- ncol(X)
# stopifnot(nrow(K) == t)
stopifnot(ncol(K) == t)
stopifnot(nrow(X) == n)
if( det(crossprod(X,X)) == 0 ) {
warning("X is singular")
return (list(REML=0,delta=0,ve=0,vg=0))
}
if(is.null(Z) ) {
if(is.null(eig.R) ) {
eig.R <- emma.eigen.R.wo.Z(K,X)
}
etas <- crossprod(eig.R$vectors,y)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,n-q,m) + matrix(delta,n-q,m,byrow=TRUE)
Etasq <- matrix(etas*etas,n-q,m)
LL <- 0.5*((n-q)*(log((n-q)/(2*pi))-1-log(colSums(Etasq/Lambdas)))-colSums(log(Lambdas)))
dLL <- 0.5*delta*((n-q)*colSums(Etasq/(Lambdas*Lambdas))/colSums(Etasq/Lambdas)-colSums(1/Lambdas))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(llim,eig.R$values,etas))
}
if( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(ulim,eig.R$values,etas))
}
for(i in 1:(m-1) )
{
if( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.REML.dLL.wo.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas=etas)
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.REML.LL.wo.Z(r$root,eig.R$values, etas))
}
}
# optdelta <- exp(optlogdelta)
}
else {
if(is.null(eig.R) ) {
eig.R <- emma.eigen.R.w.Z(Z,K,X)
}
etas <- crossprod(eig.R$vectors,y)
etas.1 <- etas[1:(t-q)]
etas.2 <- etas[(t-q+1):(n-q)]
etas.2.sq <- sum(etas.2*etas.2)
logdelta <- (0:ngrids)/ngrids*(ulim-llim)+llim
m <- length(logdelta)
delta <- exp(logdelta)
Lambdas <- matrix(eig.R$values,t-q,m) + matrix(delta,t-q,m,byrow=TRUE)
Etasq <- matrix(etas.1*etas.1,t-q,m)
dLL <- 0.5*delta*((n-q)*(colSums(Etasq/(Lambdas*Lambdas))+etas.2.sq/(delta*delta))/(colSums(Etasq/Lambdas)+etas.2.sq/delta)-(colSums(1/Lambdas)+(n-t)/delta))
optlogdelta <- vector(length=0)
optLL <- vector(length=0)
if( dLL[1] < esp ) {
optlogdelta <- append(optlogdelta, llim)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(llim,eig.R$values,etas.1,n,t,etas.2.sq))
}
if( dLL[m-1] > 0-esp ) {
optlogdelta <- append(optlogdelta, ulim)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(ulim,eig.R$values,etas.1,n,t,etas.2.sq))
}
for(i in 1:(m-1) )
{
if( ( dLL[i]*dLL[i+1] < 0 ) && ( dLL[i] > 0 ) && ( dLL[i+1] < 0 ) )
{
r <- uniroot(emma.delta.REML.dLL.w.Z, lower=logdelta[i], upper=logdelta[i+1], lambda=eig.R$values, etas.1=etas.1, n=n, t1=t, etas.2.sq = etas.2.sq )
optlogdelta <- append(optlogdelta, r$root)
optLL <- append(optLL, emma.delta.REML.LL.w.Z(r$root,eig.R$values, etas.1, n, t, etas.2.sq ))
}
}
# optdelta <- exp(optlogdelta)
}
maxdelta <- exp(optlogdelta[which.max(optLL)])
#handler of grids with NaN log
optLL=GAPIT.replaceNaN(optLL)
maxLL <- max(optLL)
if(is.null(Z) ) {
maxva <- sum(etas*etas/(eig.R$values+maxdelta))/(n-q)
}
else {
maxva <- (sum(etas.1*etas.1/(eig.R$values+maxdelta))+etas.2.sq/maxdelta)/(n-q)
}
maxve <- maxva*maxdelta
return (list(REML=maxLL,delta=maxdelta,ve=maxve,vg=maxva))
}
#=============================================================================================
`GAPIT.get.LL` <-
compiler::cmpfun(
function(pheno,geno=NULL,snp.pool,X0=NULL){
# evaluation of the maximum likelihood
#Input: ys, xs, vg, delta, Z, X0, snp.pool
#Output: LL
#Authors: Qishan Wang, Feng Tian and Zhiwu Zhang
#Last update: April 16, 2012
################################################################################
#print("GAPIT.get.LL started")
#print("dimension of pheno, snpool and X0")
#print(dim(pheno))
#print(length(pheno))
#print(dim(snp.pool))
#print(length(snp.pool))
#print(dim(X0))
#print(length(X0))
y=pheno
p=0
deltaExpStart = -5
deltaExpEnd = 5
snp.pool=snp.pool[,]
if(!is.null(snp.pool)&&var(snp.pool)==0){
deltaExpStart = 100
deltaExpEnd = deltaExpStart
#print("deltaExp change here")
}
if(is.null(X0)) {
X0 = matrix(1, nrow(snp.pool), 1)
}
#snp.test=as.numeric(geno[,1])
#X <- cbind(X0, snp.test)
X=X0
#########SVD of X
K.X.svd= svd(snp.pool,LINPACK=TRUE)######rivised by Jiabo Wang 2016.1.8
# snp.pool=NA problem occurred
#####rivised 2012.4.15 by qishan wang
d=K.X.svd$d
d=d[d>1e-08]
d=d^2
U1=K.X.svd$u
U1=U1[,1:length(d)] ##rivised 2012.4.15 by qishan wang
#handler of single snp
if(is.null(dim(U1))) U1=matrix(U1,ncol=1)
###################
n=nrow(U1)
#I= diag(1,nrow(U1)) #xiaolei removed, this costs lots of memory
U1TX=crossprod(U1,X)
U1TY=crossprod(U1,y)
yU1TY<- y-U1%*%U1TY
XU1TX<- X-U1%*%U1TX ### i is out of bracket
#xiaolei rewrite following 4 lines
IU = -tcrossprod(U1,U1)
diag(IU) = rep(1,n) + diag(IU)
#IUU=(I-tcrossprod(U1,U1))
IUX=crossprod(IU,X )
IUY=crossprod(IU,y)
#Iteration on the range of delta (-5 to 5 in glog scale)
for (m in seq(deltaExpStart,deltaExpEnd,by=0.1))
{
p=p+1
delta<- exp(m)
#----------------------------calculate beta-------------------------------------
#######get beta compnents 1
beta1=0
for(i in 1:length(d)){
one=matrix(U1TX[i,], nrow=1)
beta=crossprod(one,(one/(d[i]+delta))) #This is not real beta, confusing
beta1= beta1+beta
}
#######get beta components 2
beta2=0
for(i in 1:nrow(U1)){
one=matrix(IUX[i,], nrow=1)
dim(one)
beta=crossprod(one,one)
beta2= beta2+beta
}
beta2<-beta2/delta
#######get b3
beta3=0
for(i in 1:length(d)){
one1=matrix(U1TX[i,], nrow=1)
one2=matrix(U1TY[i,], nrow=1)
beta=crossprod(one1,(one2/(d[i]+delta))) #This is not real beta, confusing
beta3= beta3+beta
}
###########get beta4
beta4=0
for(i in 1:nrow(U1)){
one1=matrix(IUX[i,], nrow=1)
one2=matrix(IUY[i,], nrow=1)
beta=crossprod(one1,one2) #This is not real beta, confusing
beta4= beta4+beta
}
beta4<-beta4/delta
#######get final beta
#zw1=solve(beta1+beta2)
zw1 <- try(solve(beta1+beta2),silent=TRUE)
if(inherits(zw1, "try-error")){
zw1 <- ginv(beta1+beta2)
}
#zw1=ginv(beta1+beta2)
zw2=(beta3+beta4)
beta=crossprod(zw1,zw2) #This is the real beta
#----------------------------calculate LL---------------------------------------
####part 1
part11<-n*log(2*3.14)
part12<-0
for(i in 1:length(d)){
part12_pre=log(d[i]+delta)
part12= part12+part12_pre
}
part13<- (nrow(U1)-length(d))*log(delta)
part1<- -1/2*(part11+part12+part13)
###### part2
part21<-nrow(U1)
######part221
part221=0
for(i in 1:length(d)){
one1=matrix(U1TX[i,], nrow=1)
one2=matrix(U1TY[i,], nrow=1)
part221_pre=(one2-one1%*%beta)^2/(d[i]+delta) ###### beta contain covariate and snp %*%
part221= part221+part221_pre
}
######part222
part222=0
for(i in 1:n){
one1=matrix(XU1TX[i,], nrow=1)
one2=matrix(yU1TY[i,], nrow=1)
part222_pre=((one2-one1%*%beta)^2)/delta
part222= part222+part222_pre
}
part22<-n*log((1/n)*(part221+part222))
part2<- -1/2*(part21+part22)
################# likihood
LL<-part1+part2
part1<-0
part2<-0
#-----------------------Save the optimum---------------------------------------
if(p==1){
beta.save=beta
delta.save=delta
LL.save=LL
}else{
if(LL>LL.save){
beta.save=beta
delta.save=delta
LL.save=LL
}
}
} # end of Iteration on the range of delta (-5 to 5 in glog scale)
#--------------------update with the optimum------------------------------------
beta=beta.save
delta=delta.save
LL=LL.save
names(delta)=NULL
names(LL)=NULL
#--------------------calculating Va and Vem-------------------------------------
#sigma_a1
#U1TX=crossprod(U1,X)#xiaolei removed, it is re-calculated
#U1TY=crossprod(U1,y)#xiaolei removed, it is re-calculated
sigma_a1=0
for(i in 1:length(d)){
one1=matrix(U1TX[i,], nrow=1)
one2=matrix(U1TY[i,], nrow=1)
sigma_a1_pre=(one2-one1%*%beta)^2/(d[i]+delta)
sigma_a1= sigma_a1+sigma_a1_pre
}
### sigma_a2
#xiaolei removed following 3 lines
#IU=I-tcrossprod(U1,U1) #This needs to be done only once
#IUX=crossprod(IU,X)
#IUY=crossprod(IU,y)
sigma_a2=0
for(i in 1:nrow(U1)){
one1=matrix(IUX[i,], nrow=1)
one2=matrix(IUY[i,], nrow=1)
sigma_a2_pre<-(one2-one1%*%beta)^2
sigma_a2= sigma_a2+sigma_a2_pre
}
sigma_a2<-sigma_a2/delta
sigma_a<- 1/n*(sigma_a1+sigma_a2)
sigma_e<-delta*sigma_a
return(list(beta=beta, delta=delta, LL=LL, vg=sigma_a,ve=sigma_e))
}
)#end of cmpfun(
#=============================================================================================
`GAPIT.kinship.VanRaden` <-
function(snps,hasInbred=TRUE) {
# Object: To calculate the kinship matrix using the method of VanRaden (2009, J. Dairy Sci. 91:4414???C4423)
# Input: snps is n individual rows by m snps columns
# Output: n by n relationship matrix
# Authors: Zhwiu Zhang
# Last update: March 2, 2016
##############################################################################################
print("Calculating kinship with VanRaden method...")
#Remove invariants
fa=colSums(snps)/(2*nrow(snps))
index.non=fa>=1| fa<=0
snps=snps[,!index.non]
nSNP=ncol(snps)
nInd=nrow(snps)
n=nInd
##allele frequency of second allele
p=colSums(snps)/(2*nInd)
P=2*(p-.5) #Difference from .5, multiple by 2
snps=snps-1 #Change from 0/1/2 coding to -1/0/1 coding
print("substracting P...")
Z=t(snps)-P#operation on matrix and vector goes in direction of column
print("Getting X'X...")
#K=tcrossprod((snps), (snps))
K=crossprod((Z), (Z)) #Thanks to Peng Zheng, Meng Huang and Jiafa Chen for finding the problem
print("Adjusting...")
adj=2*sum(p*(1-p))
K=K/adj
print("Calculating kinship with VanRaden method: done")
return(K)
}
#=============================================================================================
`GAPIT.kinship.ZHANG` <-
function(snps,hasInbred=TRUE) {
# Object: To calculate ZHANG (Zones Harbored Adjustments of Negligent Genetic) relationship
# Authors: Zhwiu Zhang
# Last update: october 25, 2014
##############################################################################################
print("Calculating ZHANG relationship defined by Zhiwu Zhang...")
#Remove invariants
fa=colSums(snps)/(2*nrow(snps))
index.non=fa>=1| fa<=0
snps=snps[,!index.non]
het=1-abs(snps-1)
ind.sum=rowSums(het)
fi=ind.sum/(2*ncol(snps))
inbreeding=1-min(fi)
nSNP=ncol(snps)
nInd=nrow(snps)
n=nInd
snpMean= apply(snps,2,mean) #get mean for each snp
print("substracting mean...")
snps=t(snps)-snpMean #operation on matrix and vector goes in direction of column
print("Getting X'X...")
#K=tcrossprod((snps), (snps))
K=crossprod((snps), (snps))
if(is.na(K[1,1])) stop ("GAPIT says: Missing data is not allowed for numerical genotype data")
print("Adjusting...")
#Extract diagonals
i =1:n
j=(i-1)*n
index=i+j
d=K[index]
DL=min(d)
DU=max(d)
floor=min(K)
#Set range between 0 and 2
top=1+inbreeding
K=top*(K-floor)/(DU-floor)
Dmin=top*(DL-floor)/(DU-floor)
#Adjust based on expected minimum diagonal (1)
if(Dmin<1) {
print("Adjustment by the minimum diagonal")
K[index]=(K[index]-Dmin+1)/((top+1-Dmin)*.5)
K[-index]=K[-index]*(1/Dmin)
}
#Limiting the maximum offdiagonal to the top
Omax=max(K[-index])
if(Omax>top){
print("Adjustment by the minimum off diagonal")
K[-index]=K[-index]*(top/Omax)
}
print("Calculating kinship with Zhang method: done")
return(K)
}
#=============================================================================================
`GAPIT.kinship.loiselle` <-
function(snps, method="additive", use="all") {
# Object: To calculate the kinship matrix using the method of Loiselle et al. (1995)
# Authors: Alex Lipka and Hyun Min Kang
# Last update: May 31, 2011
##############################################################################################
#Number of SNP types that are 0s
n0 <- sum(snps==0,na.rm=TRUE)
#Number of heterozygote SNP types
nh <- sum(snps==0.5,na.rm=TRUE)
#Number of SNP types that are 1s
n1 <- sum(snps==1,na.rm=TRUE)
#Number of SNP types that are missing
nNA <- sum(is.na(snps))
#Self explanatory
dim(snps)[1]*dim(snps)[2]
#stopifnot(n0+nh+n1+nNA == length(snps))
#Note that the two lines in if(method == "dominant") and if(method == "recessive") are found in
#if(method == "additive"). Worry about this only if you have heterozygotes, which you do not.
if( method == "dominant" ) {
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) > 0.5),nrow(snps),ncol(snps))
snps[!is.na(snps) && (snps == 0.5)] <- flags[!is.na(snps) && (snps == 0.5)]
}
else if( method == "recessive" ) {
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) < 0.5),nrow(snps),ncol(snps))
snps[!is.na(snps) && (snps == 0.5)] <- flags[!is.na(snps) && (snps == 0.5)]
}
else if( ( method == "additive" ) && ( nh > 0 ) ) {
dsnps <- snps
rsnps <- snps
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) > 0.5),nrow(snps),ncol(snps))
dsnps[!is.na(snps) && (snps==0.5)] <- flags[is.na(snps) && (snps==0.5)]
flags <- matrix(as.double(rowMeans(snps,na.rm=TRUE) < 0.5),nrow(snps),ncol(snps))
rsnps[!is.na(snps) && (snps==0.5)] <- flags[is.na(snps) && (snps==0.5)]
snps <- rbind(dsnps,rsnps)
}
#mafs is a (# SNPs)x(# lines) matrix. The columns of mafs are identical, and the ij^th element is the average
#allele frequency for the SNP in the i^th row.
#if(use == "all") imputes missing SNP type values with the expected (average) allele frequency.
if( use == "all" ) {
mafs <- matrix(rowMeans(snps,na.rm=TRUE),nrow(snps),ncol(snps))
snps[is.na(snps)] <- mafs[is.na(snps)]
}
else if( use == "complete.obs" ) {
mafs <- matrix(rowMeans(snps,na.rm=TRUE),nrow(snps),ncol(snps))
snps <- snps[rowSums(is.na(snps))==0,]
}
mafs_comp <- 1-mafs
snps_comp <- 1-snps
n <- ncol(snps)
K <- matrix(nrow=n,ncol=n)
diag(K) <- 1
#Create the k term on page 1422 of Loiselle et al. (1995)
missing <- rep(NA, dim(snps)[1])
for(i in 1:dim(snps)[1]) {
missing[i] <- sum(is.na(snps[i,]))
}
for(i in 1:(n-1)) {
for(j in (i+1):n) {
Num_First_Term_1 <- (snps[,i]-mafs[,i])*(snps[,j]-mafs[,j])
Num_First_Term_2 <- (snps_comp[,i]-mafs_comp[,i])*(snps_comp[,j]-mafs_comp[,j])
First_Term <- sum(Num_First_Term_1)+sum(Num_First_Term_2)
Num_Second_Term_1 <- mafs[,i]*(1-mafs[,i])
Num_Second_Term_2 <- mafs_comp[,i]*(1-mafs_comp[,i])
Num_Second_Term_Bias_Correction <- 1/((2*n)-missing - 1)
Num_Second_Term <- Num_Second_Term_1 + Num_Second_Term_2
Second_Term <- sum(Num_Second_Term*Num_Second_Term_Bias_Correction)
Third_Term <- sum(Num_Second_Term)
f <- (First_Term + Second_Term)/Third_Term
K[i,j] <- f
if(K[i,j]<0) K[i,j]=0
K[j,i] <- K[i,j]
}
}
return(K)
}
#=============================================================================================
`GAPIT.kinship.separation` <-
function(PCs=NULL,EV=NULL,nPCs=0 ){
#Object: To calculate kinship from PCS
# PCs: the principal component as columns and individual as rows, the first column is taxa
# EV: Eigen values
# nPCs: the number of front PCs excluded to calculate kinship
#Output: kinship
#Authors: Huihui Li and Zhiwu Zhang
#Last update: April 17, 2012
##############################################################################################
print("Calling GAPIT.kinship.separation")
Total.number.PCs=ncol(PCs)
n=nrow(PCs)
print(Total.number.PCs)
print(n)
#Choose Total.number.PCs-nPCs PCs and EV to calculate K
sep.PCs=PCs[, (nPCs+2):(Total.number.PCs)] #first column is taxa
sep.EV=EV[(nPCs+1):Total.number.PCs]
Weighted.sep.EV=sep.EV/sum(sep.EV)
#X=t(t(sep.PCs)*Weighted.sep.EV)
X=sep.PCs
XMean= apply(X,2,mean)
X=as.matrix(X-XMean)
K=tcrossprod((X), (X))
#Extract diagonals
i =1:n
j=(i-1)*n
index=i+j
d=K[index]
DL=min(d)
DU=max(d)
floor=min(K)
K=(K-floor)/(DL-floor)
MD=(DU-floor)/(DL-floor)
if(is.na(K[1,1])) stop ("GAPIT says: Missing data is not allowed for numerical genotype data")
if(MD>2)K[index]=K[index]/(MD-1)+1
print("GAPIT.kinship.separation called succesfuly")
return (K)
}
#=============================================================================================
if(!require(gplots)) install.packages("gplots")
if(!require(LDheatmap)) install.packages("LDheatmap")
if(!require(genetics)) install.packages("genetics")
if(!require(ape)) install.packages("ape")
if(!require(compiler)) install.packages("compiler")
if(!require(EMMREML)) install.packages("EMMREML")
if(!require(scatterplot3d)) install.packages("scatterplot3d")
if(!'multtest'%in% installed.packages()[,"Package"]){
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("multtest")
BiocManager::install("snpStats")
}
##############################################################################################################################################
###MLMM - Multi-Locus Mixed Model
###SET OF FUNCTIONS TO CARRY GWAS CORRECTING FOR POPULATION STRUCTURE WHILE INCLUDING COFACTORS THROUGH A STEPWISE-REGRESSION APPROACH
#######
#
##note: require EMMA
#library(emma)
#source('emma.r')
#
##REQUIRED DATA & FORMAT
#
#PHENOTYPE - Y: a vector of length m, with names(Y)=individual names
#GENOTYPE - X: a n by m matrix, where n=number of individuals, m=number of SNPs, with rownames(X)=individual names, and colnames(X)=SNP names
#KINSHIP - K: a n by n matrix, with rownames(K)=colnames(K)=individual names
#each of these data being sorted in the same way, according to the individual name
#
##FOR PLOTING THE GWAS RESULTS
#SNP INFORMATION - snp_info: a data frame having at least 3 columns:
# - 1 named 'SNP', with SNP names (same as colnames(X)),
# - 1 named 'Chr', with the chromosome number to which belong each SNP
# - 1 named 'Pos', with the position of the SNP onto the chromosome it belongs to.
#######
#
##FUNCTIONS USE
#save this file somewhere on your computer and source it!
#source('path/mlmm.r')
#
###FORWARD + BACKWARD ANALYSES
#mygwas<-mlmm(Y,X,K,nbchunks,maxsteps)
#X,Y,K as described above
#nbchunks: an integer defining the number of chunks of X to run the analysis, allows to decrease the memory usage ==> minimum=2, increase it if you do not have enough memory
#maxsteps: maximum number of steps desired in the forward approach. The forward approach breaks automatically once the pseudo-heritability is close to 0,
# however to avoid doing too many steps in case the pseudo-heritability does not reach a value close to 0, this parameter is also used.
# It's value must be specified as an integer >= 3
#
###RESULTS
#
##STEPWISE TABLE
#mygwas$step_table
#
##PLOTS
#
##PLOTS FORM THE FORWARD TABLE
#plot_step_table(mygwas,type=c('h2','maxpval','BIC','extBIC'))
#
##RSS PLOT
#plot_step_RSS(mygwas)
#
##GWAS MANHATTAN PLOTS
#
#FORWARD STEPS
#plot_fwd_GWAS(mygwas,step,snp_info,pval_filt)
#step=the step to be plotted in the forward approach, where 1 is the EMMAX scan (no cofactor)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#
#OPTIMAL MODELS
#Automatic identification of the optimal models within the forwrad-backward models according to the extendedBIC or multiple-bonferonni criteria
#
#plot_opt_GWAS(mygwas,opt=c('extBIC','mbonf'),snp_info,pval_filt)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#
##GWAS MANHATTAN PLOT ZOOMED IN A REGION OF INTEREST
#plot_fwd_region(mygwas,step,snp_info,pval_filt,chrom,pos1,pos2)
#step=the step to be plotted in the forward approach, where 1 is the EMMAX scan (no cofactor)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#chrom is an integer specifying the chromosome on which the region of interest is
#pos1, pos2 are integers delimiting the region of interest in the same unit as Pos in snp_info
#
#plot_opt_region(mygwas,opt=c('extBIC','mbonf'),snp_info,pval_filt,chrom,pos1,pos2)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#chrom is an integer specifying the chromosome on which the region of interest is
#pos1, pos2 are integers delimiting the region of interest in the same unit as Pos in snp_info
#
##QQPLOTS of pvalues
#qqplot_fwd_GWAS(mygwas,nsteps)
#nsteps=maximum number of forward steps to be displayed
#
#qqplot_opt_GWAS(mygwas,opt=c('extBIC','mbonf'))
#
##############################################################################################################################################
mlmm<-function(Y,X,K,nbchunks,maxsteps,thresh = NULL) {
n<-length(Y)
m<-ncol(X)
stopifnot(ncol(K) == n)
stopifnot(nrow(K) == n)
stopifnot(nrow(X) == n)
stopifnot(nbchunks >= 2)
stopifnot(maxsteps >= 3)
#INTERCEPT
Xo<-rep(1,n)
#K MATRIX NORMALISATION
K_norm<-(n-1)/sum((diag(n)-matrix(1,n,n)/n)*K)*K
rm(K)
#step 0 : NULL MODEL
cof_fwd<-list()
cof_fwd[[1]]<-as.matrix(Xo)
colnames(cof_fwd[[1]])<-'Xo'
mod_fwd<-list()
mod_fwd[[1]]<-emma.REMLE(Y,cof_fwd[[1]],K_norm)
herit_fwd<-list()
herit_fwd[[1]]<-mod_fwd[[1]]$vg/(mod_fwd[[1]]$vg+mod_fwd[[1]]$ve)
RSSf<-list()
RSSf[[1]]<-'NA'
RSS_H0<-list()
RSS_H0[[1]]<-'NA'
df1<-1
df2<-list()
df2[[1]]<-'NA'
Ftest<-list()
Ftest[[1]]<-'NA'
pval<-list()
pval[[1]]<-'NA'
fwd_lm<-list()
cat('null model done! pseudo-h=',round(herit_fwd[[1]],3),'\n')
#step 1 : EMMAX
M<-solve(chol(mod_fwd[[1]]$vg*K_norm+mod_fwd[[1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cof_fwd[[1]])
fwd_lm[[1]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[1]]$residuals
Q_<-qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[1]])])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[1]])])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[1]])-1))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[2]]<-unlist(RSS)
RSS_H0[[2]]<-sum(Res_H0^2)
df2[[2]]<-n-df1-ncol(cof_fwd[[1]])
Ftest[[2]]<-(rep(RSS_H0[[2]],length(RSSf[[2]]))/RSSf[[2]]-1)*df2[[2]]/df1
pval[[2]]<-pf(Ftest[[2]],df1,df2[[2]],lower.tail=FALSE)
cof_fwd[[2]]<-cbind(cof_fwd[[1]],X[,colnames(X) %in% names(which(RSSf[[2]]==min(RSSf[[2]]))[1])])
colnames(cof_fwd[[2]])<-c(colnames(cof_fwd[[1]]),names(which(RSSf[[2]]==min(RSSf[[2]]))[1]))
mod_fwd[[2]]<-emma.REMLE(Y,cof_fwd[[2]],K_norm)
herit_fwd[[2]]<-mod_fwd[[2]]$vg/(mod_fwd[[2]]$vg+mod_fwd[[2]]$ve)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)
cat('step 1 done! pseudo-h=',round(herit_fwd[[2]],3),'\n')
#FORWARD
for (i in 3:(maxsteps)) {
if (herit_fwd[[i-2]] < 0.01) break else {
M<-solve(chol(mod_fwd[[i-1]]$vg*K_norm+mod_fwd[[i-1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cof_fwd[[i-1]])
fwd_lm[[i-1]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[i-1]]$residuals
Q_ <- qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[i-1]])])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[i-1]])])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[i-1]])-1))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[i]]<-unlist(RSS)
RSS_H0[[i]]<-sum(Res_H0^2)
df2[[i]]<-n-df1-ncol(cof_fwd[[i-1]])
Ftest[[i]]<-(rep(RSS_H0[[i]],length(RSSf[[i]]))/RSSf[[i]]-1)*df2[[i]]/df1
pval[[i]]<-pf(Ftest[[i]],df1,df2[[i]],lower.tail=FALSE)
cof_fwd[[i]]<-cbind(cof_fwd[[i-1]],X[,colnames(X) %in% names(which(RSSf[[i]]==min(RSSf[[i]]))[1])])
colnames(cof_fwd[[i]])<-c(colnames(cof_fwd[[i-1]]),names(which(RSSf[[i]]==min(RSSf[[i]]))[1]))
mod_fwd[[i]]<-emma.REMLE(Y,cof_fwd[[i]],K_norm)
herit_fwd[[i]]<-mod_fwd[[i]]$vg/(mod_fwd[[i]]$vg+mod_fwd[[i]]$ve)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)}
cat('step ',i-1,' done! pseudo-h=',round(herit_fwd[[i]],3),'\n')}
rm(i)
##gls at last forward step
M<-solve(chol(mod_fwd[[length(mod_fwd)]]$vg*K_norm+mod_fwd[[length(mod_fwd)]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cof_fwd[[length(mod_fwd)]])
fwd_lm[[length(mod_fwd)]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[length(mod_fwd)]]$residuals
Q_ <- qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[length(mod_fwd)]])])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[length(mod_fwd)]])])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[length(mod_fwd)]])-1))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[length(mod_fwd)+1]]<-unlist(RSS)
RSS_H0[[length(mod_fwd)+1]]<-sum(Res_H0^2)
df2[[length(mod_fwd)+1]]<-n-df1-ncol(cof_fwd[[length(mod_fwd)]])
Ftest[[length(mod_fwd)+1]]<-(rep(RSS_H0[[length(mod_fwd)+1]],length(RSSf[[length(mod_fwd)+1]]))/RSSf[[length(mod_fwd)+1]]-1)*df2[[length(mod_fwd)+1]]/df1
pval[[length(mod_fwd)+1]]<-pf(Ftest[[length(mod_fwd)+1]],df1,df2[[length(mod_fwd)+1]],lower.tail=FALSE)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)
##get max pval at each forward step
max_pval_fwd<-vector(mode="numeric",length=length(fwd_lm))
max_pval_fwd[1]<-0
for (i in 2:length(fwd_lm)) {max_pval_fwd[i]<-max(fwd_lm[[i]]$coef[2:i,4])}
rm(i)
##get the number of parameters & Loglikelihood from ML at each step
mod_fwd_LL<-list()
mod_fwd_LL[[1]]<-list(nfixed=ncol(cof_fwd[[1]]),LL=emma.MLE(Y,cof_fwd[[1]],K_norm)$ML)
for (i in 2:length(cof_fwd)) {mod_fwd_LL[[i]]<-list(nfixed=ncol(cof_fwd[[i]]),LL=emma.MLE(Y,cof_fwd[[i]],K_norm)$ML)}
rm(i)
cat('backward analysis','\n')
##BACKWARD (1st step == last fwd step)
dropcof_bwd<-list()
cof_bwd<-list()
mod_bwd <- list()
bwd_lm<-list()
herit_bwd<-list()
dropcof_bwd[[1]]<-'NA'
cof_bwd[[1]]<-as.matrix(cof_fwd[[length(mod_fwd)]][,!colnames(cof_fwd[[length(mod_fwd)]]) %in% dropcof_bwd[[1]]])
colnames(cof_bwd[[1]])<-colnames(cof_fwd[[length(mod_fwd)]])[!colnames(cof_fwd[[length(mod_fwd)]]) %in% dropcof_bwd[[1]]]
mod_bwd[[1]]<-emma.REMLE(Y,cof_bwd[[1]],K_norm)
herit_bwd[[1]]<-mod_bwd[[1]]$vg/(mod_bwd[[1]]$vg+mod_bwd[[1]]$ve)
M<-solve(chol(mod_bwd[[1]]$vg*K_norm+mod_bwd[[1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_bwd_t<-crossprod(M,cof_bwd[[1]])
bwd_lm[[1]]<-summary(lm(Y_t~0+cof_bwd_t))
rm(M,Y_t,cof_bwd_t)
for (i in 2:length(mod_fwd)) {
dropcof_bwd[[i]]<-(colnames(cof_bwd[[i-1]])[2:ncol(cof_bwd[[i-1]])])[which(abs(bwd_lm[[i-1]]$coef[2:nrow(bwd_lm[[i-1]]$coef),3])==min(abs(bwd_lm[[i-1]]$coef[2:nrow(bwd_lm[[i-1]]$coef),3])))]
cof_bwd[[i]]<-as.matrix(cof_bwd[[i-1]][,!colnames(cof_bwd[[i-1]]) %in% dropcof_bwd[[i]]])
colnames(cof_bwd[[i]])<-colnames(cof_bwd[[i-1]])[!colnames(cof_bwd[[i-1]]) %in% dropcof_bwd[[i]]]
mod_bwd[[i]]<-emma.REMLE(Y,cof_bwd[[i]],K_norm)
herit_bwd[[i]]<-mod_bwd[[i]]$vg/(mod_bwd[[i]]$vg+mod_bwd[[i]]$ve)
M<-solve(chol(mod_bwd[[i]]$vg*K_norm+mod_bwd[[i]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_bwd_t<-crossprod(M,cof_bwd[[i]])
bwd_lm[[i]]<-summary(lm(Y_t~0+cof_bwd_t))
rm(M,Y_t,cof_bwd_t)}
rm(i)
##get max pval at each backward step
max_pval_bwd<-vector(mode="numeric",length=length(bwd_lm))
for (i in 1:(length(bwd_lm)-1)) {max_pval_bwd[i]<-max(bwd_lm[[i]]$coef[2:(length(bwd_lm)+1-i),4])}
max_pval_bwd[length(bwd_lm)]<-0
##get the number of parameters & Loglikelihood from ML at each step
mod_bwd_LL<-list()
mod_bwd_LL[[1]]<-list(nfixed=ncol(cof_bwd[[1]]),LL=emma.MLE(Y,cof_bwd[[1]],K_norm)$ML)
for (i in 2:length(cof_bwd)) {mod_bwd_LL[[i]]<-list(nfixed=ncol(cof_bwd[[i]]),LL=emma.MLE(Y,cof_bwd[[i]],K_norm)$ML)}
rm(i)
cat('creating output','\n')
##Forward Table: Fwd + Bwd Tables
#Compute parameters for model criteria
BIC<-function(x){-2*x$LL+(x$nfixed+1)*log(n)}
extBIC<-function(x){BIC(x)+2*lchoose(m,x$nfixed-1)}
fwd_table<-data.frame(step=ncol(cof_fwd[[1]])-1,step_=paste('fwd',ncol(cof_fwd[[1]])-1,sep=''),cof='NA',ncof=ncol(cof_fwd[[1]])-1,h2=herit_fwd[[1]]
,maxpval=max_pval_fwd[1],BIC=BIC(mod_fwd_LL[[1]]),extBIC=extBIC(mod_fwd_LL[[1]]))
for (i in 2:(length(mod_fwd))) {fwd_table<-rbind(fwd_table,
data.frame(step=ncol(cof_fwd[[i]])-1,step_=paste('fwd',ncol(cof_fwd[[i]])-1,sep=''),cof=paste('+',colnames(cof_fwd[[i]])[i],sep=''),ncof=ncol(cof_fwd[[i]])-1,h2=herit_fwd[[i]]
,maxpval=max_pval_fwd[i],BIC=BIC(mod_fwd_LL[[i]]),extBIC=extBIC(mod_fwd_LL[[i]])))}
rm(i)
bwd_table<-data.frame(step=length(mod_fwd),step_=paste('bwd',0,sep=''),cof=paste('-',dropcof_bwd[[1]],sep=''),ncof=ncol(cof_bwd[[1]])-1,h2=herit_bwd[[1]]
,maxpval=max_pval_bwd[1],BIC=BIC(mod_bwd_LL[[1]]),extBIC=extBIC(mod_bwd_LL[[1]]))
for (i in 2:(length(mod_bwd))) {bwd_table<-rbind(bwd_table,
data.frame(step=length(mod_fwd)+i-1,step_=paste('bwd',i-1,sep=''),cof=paste('-',dropcof_bwd[[i]],sep=''),ncof=ncol(cof_bwd[[i]])-1,h2=herit_bwd[[i]]
,maxpval=max_pval_bwd[i],BIC=BIC(mod_bwd_LL[[i]]),extBIC=extBIC(mod_bwd_LL[[i]])))}
rm(i,BIC,extBIC,max_pval_fwd,max_pval_bwd,dropcof_bwd)
fwdbwd_table<-rbind(fwd_table,bwd_table)
#RSS for plot
mod_fwd_RSS<-vector()
mod_fwd_RSS[1]<-sum((Y-cof_fwd[[1]]%*%fwd_lm[[1]]$coef[,1])^2)
for (i in 2:length(mod_fwd)) {mod_fwd_RSS[i]<-sum((Y-cof_fwd[[i]]%*%fwd_lm[[i]]$coef[,1])^2)}
mod_bwd_RSS<-vector()
mod_bwd_RSS[1]<-sum((Y-cof_bwd[[1]]%*%bwd_lm[[1]]$coef[,1])^2)
for (i in 2:length(mod_bwd)) {mod_bwd_RSS[i]<-sum((Y-cof_bwd[[i]]%*%bwd_lm[[i]]$coef[,1])^2)}
expl_RSS<-c(1-sapply(mod_fwd_RSS,function(x){x/mod_fwd_RSS[1]}),1-sapply(mod_bwd_RSS,function(x){x/mod_bwd_RSS[length(mod_bwd_RSS)]}))
h2_RSS<-c(unlist(herit_fwd),unlist(herit_bwd))*(1-expl_RSS)
unexpl_RSS<-1-expl_RSS-h2_RSS
plot_RSS<-t(apply(cbind(expl_RSS,h2_RSS,unexpl_RSS),1,cumsum))
#GLS pvals at each step
pval_step<-list()
pval_step[[1]]<-list(out=data.frame("SNP"=colnames(X),"pval"=pval[[2]]),"cof"=NA, "coef"=fwd_lm[[1]]$coef)
for (i in 2:(length(mod_fwd))) {pval_step[[i]]<-list(out=rbind(data.frame(SNP=colnames(cof_fwd[[i]])[-1],'pval'=fwd_lm[[i]]$coef[2:i,4]),
data.frame(SNP=colnames(X)[-which(colnames(X) %in% colnames(cof_fwd[[i]]))],'pval'=pval[[i+1]])),"cof"=colnames(cof_fwd[[i]])[-1], "coef"=fwd_lm[[i]]$coef)}
#GLS pvals for best models according to extBIC and mbonf
opt_extBIC<-fwdbwd_table[which(fwdbwd_table$extBIC==min(fwdbwd_table$extBIC))[1],]
opt_mbonf<-(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),])[which(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),]$ncof==max(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),]$ncof))[1],]
if(! is.null(thresh)){
opt_thresh<-(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),])[which(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),]$ncof==max(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),]$ncof))[1],]
}
bestmodel_pvals<-function(model) {if(substr(model$step_,start=0,stop=3)=='fwd') {
pval_step[[as.integer(substring(model$step_,first=4))+1]]} else if (substr(model$step_,start=0,stop=3)=='bwd') {
cof<-cof_bwd[[as.integer(substring(model$step_,first=4))+1]]
mixedmod<-emma.REMLE(Y,cof,K_norm)
M<-solve(chol(mixedmod$vg*K_norm+mixedmod$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_t<-crossprod(M,cof)
GLS_lm<-summary(lm(Y_t~0+cof_t))
Res_H0<-GLS_lm$residuals
Q_ <- qr.Q(qr(cof_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof)])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof)])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof)-1))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf<-unlist(RSS)
RSS_H0<-sum(Res_H0^2)
df2<-n-df1-ncol(cof)
Ftest<-(rep(RSS_H0,length(RSSf))/RSSf-1)*df2/df1
pval<-pf(Ftest,df1,df2,lower.tail=FALSE)
list('out'=rbind(data.frame(SNP=colnames(cof)[-1],'pval'=GLS_lm$coef[2:(ncol(cof)),4]),
data.frame('SNP'=colnames(X)[-which(colnames(X) %in% colnames(cof))],'pval'=pval)),
'cof'=colnames(cof)[-1],
'coef'=GLS_lm$coef)} else {cat('error \n')}}
opt_extBIC_out<-bestmodel_pvals(opt_extBIC)
opt_mbonf_out<-bestmodel_pvals(opt_mbonf)
if(! is.null(thresh)){
opt_thresh_out<-bestmodel_pvals(opt_thresh)
}
output <- list(step_table=fwdbwd_table,pval_step=pval_step,RSSout=plot_RSS,bonf_thresh=-log10(0.05/m),opt_extBIC=opt_extBIC_out,opt_mbonf=opt_mbonf_out)
if(! is.null(thresh)){
output$thresh <- -log10(thresh)
output$opt_thresh <- opt_thresh_out
}
return(output)
}
##############################################################################################################################################
###MLMM_COF - Multi-Locus Mixed Model
###SET OF FUNCTIONS TO CARRY GWAS CORRECTING FOR POPULATION STRUCTURE WHILE INCLUDING COFACTORS THROUGH A STEPWISE-REGRESSION APPROACH
#######
#
##note: require EMMA
#library(emma)
#source('emma.r')
#
##REQUIRED DATA & FORMAT
#
#PHENOTYPE - Y: a vector of length m, with names(Y)=individual names
#GENOTYPE - X: a n by m matrix, where n=number of individuals, m=number of SNPs, with rownames(X)=individual names, and colnames(X)=SNP names
#KINSHIP - K: a n by n matrix, with rownames(K)=colnames(K)=individual names
#COVARIANCE MATRIX - cofs: a n by p matrix, where n=number of individuals, p=number of covariates in the matrix (e.g. PC axes)
#each of these data being sorted in the same way, according to the individual name
#
##FOR PLOTING THE GWAS RESULTS
#SNP INFORMATION - snp_info: a data frame having at least 3 columns:
# - 1 named 'SNP', with SNP names (same as colnames(X)),
# - 1 named 'Chr', with the chromosome number to which belong each SNP
# - 1 named 'Pos', with the position of the SNP onto the chromosome it belongs to.
#######
#
##FUNCTIONS USE
#save this file somewhere on your computer and source it!
#source('path/mlmm.r')
#
###FORWARD + BACKWARD ANALYSES
#mygwas<-mlmm_cof(Y,X,K,nbchunks,maxsteps)
#X,Y,K as described above
#nbchunks: an integer defining the number of chunks of X to run the analysis, allows to decrease the memory usage ==> minimum=2, increase it if you do not have enough memory
#maxsteps: maximum number of steps desired in the forward approach. The forward approach breaks automatically once the pseudo-heritability is close to 0,
# however to avoid doing too many steps in case the pseudo-heritability does not reach a value close to 0, this parameter is also used.
# It's value must be specified as an integer >= 3
#
###RESULTS
#
##STEPWISE TABLE
#mygwas$step_table
#
##PLOTS
#
##PLOTS FORM THE FORWARD TABLE
#plot_step_table(mygwas,type=c('h2','maxpval','BIC','extBIC'))
#
##RSS PLOT
#plot_step_RSS(mygwas)
#
##GWAS MANHATTAN PLOTS
#
#FORWARD STEPS
#plot_fwd_GWAS(mygwas,step,snp_info,pval_filt)
#step=the step to be plotted in the forward approach, where 1 is the EMMAX scan (no cofactor)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#
#OPTIMAL MODELS
#Automatic identification of the optimal models within the forwrad-backward models according to the extendedBIC or multiple-bonferonni criteria
#
#plot_opt_GWAS(mygwas,opt=c('extBIC','mbonf'),snp_info,pval_filt)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#
##GWAS MANHATTAN PLOT ZOOMED IN A REGION OF INTEREST
#plot_fwd_region(mygwas,step,snp_info,pval_filt,chrom,pos1,pos2)
#step=the step to be plotted in the forward approach, where 1 is the EMMAX scan (no cofactor)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#chrom is an integer specifying the chromosome on which the region of interest is
#pos1, pos2 are integers delimiting the region of interest in the same unit as Pos in snp_info
#
#plot_opt_region(mygwas,opt=c('extBIC','mbonf'),snp_info,pval_filt,chrom,pos1,pos2)
#snp_info as described above
#pval_filt=a p-value threshold for filtering the output, only p-vals below this threshold will be displayed in the plot
#chrom is an integer specifying the chromosome on which the region of interest is
#pos1, pos2 are integers delimiting the region of interest in the same unit as Pos in snp_info
#
##QQPLOTS of pvalues
#qqplot_fwd_GWAS(mygwas,nsteps)
#nsteps=maximum number of forward steps to be displayed
#
#qqplot_opt_GWAS(mygwas,opt=c('extBIC','mbonf'))
#
##############################################################################################################################################
mlmm_cof<-function(Y,X,cofs,K,nbchunks,maxsteps,thresh = NULL) {
n<-length(Y)
m<-ncol(X)
stopifnot(ncol(K) == n)
stopifnot(nrow(K) == n)
stopifnot(nrow(X) == n)
stopifnot(nrow(cofs) == n)
stopifnot(nbchunks >= 2)
stopifnot(maxsteps >= 3)
#INTERCEPT
Xo<-rep(1,n)
#K MATRIX NORMALISATION
K_norm<-(n-1)/sum((diag(n)-matrix(1,n,n)/n)*K)*K
rm(K)
#step 0 : NULL MODEL
fix_cofs<-cbind(Xo,cofs)
rm(cofs)
addcof_fwd<-list()
addcof_fwd[[1]]<-'NA'
cof_fwd<-list()
cof_fwd[[1]]<-as.matrix(X[,colnames(X) %in% addcof_fwd[[1]]])
mod_fwd<-list()
mod_fwd[[1]]<-emma.REMLE(Y,cbind(fix_cofs,cof_fwd[[1]]),K_norm)
herit_fwd<-list()
herit_fwd[[1]]<-mod_fwd[[1]]$vg/(mod_fwd[[1]]$vg+mod_fwd[[1]]$ve)
RSSf<-list()
RSSf[[1]]<-'NA'
RSS_H0<-list()
RSS_H0[[1]]<-'NA'
df1<-1
df2<-list()
df2[[1]]<-'NA'
Ftest<-list()
Ftest[[1]]<-'NA'
pval<-list()
pval[[1]]<-'NA'
fwd_lm<-list()
cat('null model done! pseudo-h=',round(herit_fwd[[1]],3),'\n')
#step 1 : EMMAX
M<-solve(chol(mod_fwd[[1]]$vg*K_norm+mod_fwd[[1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cbind(fix_cofs,cof_fwd[[1]]))
fwd_lm[[1]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[1]]$residuals
Q_<-qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% addcof_fwd[[1]]])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% addcof_fwd[[1]]])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[1]])))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[2]]<-unlist(RSS)
RSS_H0[[2]]<-sum(Res_H0^2)
df2[[2]]<-n-df1-ncol(fix_cofs)-ncol(cof_fwd[[1]])
Ftest[[2]]<-(rep(RSS_H0[[2]],length(RSSf[[2]]))/RSSf[[2]]-1)*df2[[2]]/df1
pval[[2]]<-pf(Ftest[[2]],df1,df2[[2]],lower.tail=FALSE)
addcof_fwd[[2]]<-names(which(RSSf[[2]]==min(RSSf[[2]]))[1])
cof_fwd[[2]]<-cbind(cof_fwd[[1]],X[,colnames(X) %in% addcof_fwd[[2]]])
colnames(cof_fwd[[2]])[ncol(cof_fwd[[2]])]<-addcof_fwd[[2]]
mod_fwd[[2]]<-emma.REMLE(Y,cbind(fix_cofs,cof_fwd[[2]]),K_norm)
herit_fwd[[2]]<-mod_fwd[[2]]$vg/(mod_fwd[[2]]$vg+mod_fwd[[2]]$ve)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)
cat('step 1 done! pseudo-h=',round(herit_fwd[[2]],3),'\n')
#FORWARD
for (i in 3:(maxsteps)) {
if (herit_fwd[[i-2]] < 0.01) break else {
M<-solve(chol(mod_fwd[[i-1]]$vg*K_norm+mod_fwd[[i-1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cbind(fix_cofs,cof_fwd[[i-1]]))
fwd_lm[[i-1]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[i-1]]$residuals
Q_ <- qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[i-1]])])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[i-1]])])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[i-1]])))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[i]]<-unlist(RSS)
RSS_H0[[i]]<-sum(Res_H0^2)
df2[[i]]<-n-df1-ncol(fix_cofs)-ncol(cof_fwd[[i-1]])
Ftest[[i]]<-(rep(RSS_H0[[i]],length(RSSf[[i]]))/RSSf[[i]]-1)*df2[[i]]/df1
pval[[i]]<-pf(Ftest[[i]],df1,df2[[i]],lower.tail=FALSE)
addcof_fwd[[i]]<-names(which(RSSf[[i]]==min(RSSf[[i]]))[1])
cof_fwd[[i]]<-cbind(cof_fwd[[i-1]],X[,colnames(X) %in% addcof_fwd[[i]]])
colnames(cof_fwd[[i]])[ncol(cof_fwd[[i]])]<-addcof_fwd[[i]]
mod_fwd[[i]]<-emma.REMLE(Y,cbind(fix_cofs,cof_fwd[[i]]),K_norm)
herit_fwd[[i]]<-mod_fwd[[i]]$vg/(mod_fwd[[i]]$vg+mod_fwd[[i]]$ve)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)}
cat('step ',i-1,' done! pseudo-h=',round(herit_fwd[[i]],3),'\n')}
rm(i)
##gls at last forward step
M<-solve(chol(mod_fwd[[length(mod_fwd)]]$vg*K_norm+mod_fwd[[length(mod_fwd)]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_fwd_t<-crossprod(M,cbind(fix_cofs,cof_fwd[[length(mod_fwd)]]))
fwd_lm[[length(mod_fwd)]]<-summary(lm(Y_t~0+cof_fwd_t))
Res_H0<-fwd_lm[[length(mod_fwd)]]$residuals
Q_ <- qr.Q(qr(cof_fwd_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[length(mod_fwd)]])])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof_fwd[[length(mod_fwd)]])])[,((j)*round(m/nbchunks)+1):(m-(ncol(cof_fwd[[length(mod_fwd)]])))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf[[length(mod_fwd)+1]]<-unlist(RSS)
RSS_H0[[length(mod_fwd)+1]]<-sum(Res_H0^2)
df2[[length(mod_fwd)+1]]<-n-df1-ncol(fix_cofs)-ncol(cof_fwd[[length(mod_fwd)]])
Ftest[[length(mod_fwd)+1]]<-(rep(RSS_H0[[length(mod_fwd)+1]],length(RSSf[[length(mod_fwd)+1]]))/RSSf[[length(mod_fwd)+1]]-1)*df2[[length(mod_fwd)+1]]/df1
pval[[length(mod_fwd)+1]]<-pf(Ftest[[length(mod_fwd)+1]],df1,df2[[length(mod_fwd)+1]],lower.tail=FALSE)
rm(M,Y_t,cof_fwd_t,Res_H0,Q_,RSS)
##get max pval at each forward step
max_pval_fwd<-vector(mode="numeric",length=length(fwd_lm))
max_pval_fwd[1]<-0
for (i in 2:length(fwd_lm)) {max_pval_fwd[i]<-max(fwd_lm[[i]]$coef[(ncol(fix_cofs)+1):(ncol(fix_cofs)+ncol(cof_fwd[[i]])),4])}
rm(i)
##get the number of parameters & Loglikelihood from ML at each step
mod_fwd_LL<-list()
mod_fwd_LL[[1]]<-list(nfixed=ncol(cbind(fix_cofs,cof_fwd[[1]])),LL=emma.MLE(Y,cbind(fix_cofs,cof_fwd[[1]]),K_norm)$ML)
for (i in 2:length(cof_fwd)) {mod_fwd_LL[[i]]<-list(nfixed=ncol(cbind(fix_cofs,cof_fwd[[i]])),LL=emma.MLE(Y,cbind(fix_cofs,cof_fwd[[i]]),K_norm)$ML)}
rm(i)
cat('backward analysis','\n')
##BACKWARD (1st step == last fwd step)
dropcof_bwd<-list()
cof_bwd<-list()
mod_bwd <- list()
bwd_lm<-list()
herit_bwd<-list()
dropcof_bwd[[1]]<-'NA'
cof_bwd[[1]]<-as.matrix(cof_fwd[[length(mod_fwd)]][,!colnames(cof_fwd[[length(mod_fwd)]]) %in% dropcof_bwd[[1]]])
colnames(cof_bwd[[1]])<-colnames(cof_fwd[[length(mod_fwd)]])[!colnames(cof_fwd[[length(mod_fwd)]]) %in% dropcof_bwd[[1]]]
mod_bwd[[1]]<-emma.REMLE(Y,cbind(fix_cofs,cof_bwd[[1]]),K_norm)
herit_bwd[[1]]<-mod_bwd[[1]]$vg/(mod_bwd[[1]]$vg+mod_bwd[[1]]$ve)
M<-solve(chol(mod_bwd[[1]]$vg*K_norm+mod_bwd[[1]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_bwd_t<-crossprod(M,cbind(fix_cofs,cof_bwd[[1]]))
bwd_lm[[1]]<-summary(lm(Y_t~0+cof_bwd_t))
rm(M,Y_t,cof_bwd_t)
for (i in 2:length(mod_fwd)) {
dropcof_bwd[[i]]<-colnames(cof_bwd[[i-1]])[which(abs(bwd_lm[[i-1]]$coef[(ncol(fix_cofs)+1):nrow(bwd_lm[[i-1]]$coef),3])==min(abs(bwd_lm[[i-1]]$coef[(ncol(fix_cofs)+1):nrow(bwd_lm[[i-1]]$coef),3])))]
cof_bwd[[i]]<-as.matrix(cof_bwd[[i-1]][,!colnames(cof_bwd[[i-1]]) %in% dropcof_bwd[[i]]])
colnames(cof_bwd[[i]])<-colnames(cof_bwd[[i-1]])[!colnames(cof_bwd[[i-1]]) %in% dropcof_bwd[[i]]]
mod_bwd[[i]]<-emma.REMLE(Y,cbind(fix_cofs,cof_bwd[[i]]),K_norm)
herit_bwd[[i]]<-mod_bwd[[i]]$vg/(mod_bwd[[i]]$vg+mod_bwd[[i]]$ve)
M<-solve(chol(mod_bwd[[i]]$vg*K_norm+mod_bwd[[i]]$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_bwd_t<-crossprod(M,cbind(fix_cofs,cof_bwd[[i]]))
bwd_lm[[i]]<-summary(lm(Y_t~0+cof_bwd_t))
rm(M,Y_t,cof_bwd_t)}
rm(i)
##get max pval at each backward step
max_pval_bwd<-vector(mode="numeric",length=length(bwd_lm))
for (i in 1:(length(bwd_lm)-1)) {max_pval_bwd[i]<-max(bwd_lm[[i]]$coef[(ncol(fix_cofs)+1):(ncol(fix_cofs)+ncol(cof_bwd[[i]])),4])}
max_pval_bwd[length(bwd_lm)]<-0
##get the number of parameters & Loglikelihood from ML at each step
mod_bwd_LL<-list()
mod_bwd_LL[[1]]<-list(nfixed=ncol(cbind(fix_cofs,cof_bwd[[1]])),LL=emma.MLE(Y,cbind(fix_cofs,cof_bwd[[1]]),K_norm)$ML)
for (i in 2:length(cof_bwd)) {mod_bwd_LL[[i]]<-list(nfixed=ncol(cbind(fix_cofs,cof_bwd[[i]])),LL=emma.MLE(Y,cbind(fix_cofs,cof_bwd[[i]]),K_norm)$ML)}
rm(i)
cat('creating output','\n')
##Forward Table: Fwd + Bwd Tables
#Compute parameters for model criteria
BIC<-function(x){-2*x$LL+(x$nfixed+1)*log(n)}
extBIC<-function(x){BIC(x)+2*lchoose(m,x$nfixed-1)}
fwd_table<-data.frame(step=ncol(cof_fwd[[1]]),step_=paste('fwd',ncol(cof_fwd[[1]]),sep=''),cof=paste('+',addcof_fwd[[1]],sep=''),ncof=ncol(cof_fwd[[1]]),h2=herit_fwd[[1]]
,maxpval=max_pval_fwd[1],BIC=BIC(mod_fwd_LL[[1]]),extBIC=extBIC(mod_fwd_LL[[1]]))
for (i in 2:(length(mod_fwd))) {fwd_table<-rbind(fwd_table,
data.frame(step=ncol(cof_fwd[[i]]),step_=paste('fwd',ncol(cof_fwd[[i]]),sep=''),cof=paste('+',addcof_fwd[[i]],sep=''),ncof=ncol(cof_fwd[[i]]),h2=herit_fwd[[i]]
,maxpval=max_pval_fwd[i],BIC=BIC(mod_fwd_LL[[i]]),extBIC=extBIC(mod_fwd_LL[[i]])))}
rm(i)
bwd_table<-data.frame(step=length(mod_fwd),step_=paste('bwd',0,sep=''),cof=paste('-',dropcof_bwd[[1]],sep=''),ncof=ncol(cof_bwd[[1]]),h2=herit_bwd[[1]]
,maxpval=max_pval_bwd[1],BIC=BIC(mod_bwd_LL[[1]]),extBIC=extBIC(mod_bwd_LL[[1]]))
for (i in 2:(length(mod_bwd))) {bwd_table<-rbind(bwd_table,
data.frame(step=length(mod_fwd)+i-1,step_=paste('bwd',i-1,sep=''),cof=paste('-',dropcof_bwd[[i]],sep=''),ncof=ncol(cof_bwd[[i]]),h2=herit_bwd[[i]]
,maxpval=max_pval_bwd[i],BIC=BIC(mod_bwd_LL[[i]]),extBIC=extBIC(mod_bwd_LL[[i]])))}
rm(i,BIC,extBIC,max_pval_fwd,max_pval_bwd,dropcof_bwd)
fwdbwd_table<-rbind(fwd_table,bwd_table)
#RSS for plot
#null model only with intercept
null<-emma.REMLE(Y,as.matrix(Xo),K_norm)
M<-solve(chol(null$vg*K_norm+null$ve*diag(n)))
Y_t<-crossprod(M,Y)
Xo_t<-crossprod(M,as.matrix(Xo))
null_lm<-summary(lm(Y_t~0+Xo_t))
rm(null,M,Y_t,Xo_t)
RSS_null<-sum((Y-as.matrix(Xo)%*%null_lm$coef[,1])^2)
mod_fwd_RSS<-vector()
mod_fwd_RSS[1]<-sum((Y-cbind(fix_cofs,cof_fwd[[1]])%*%fwd_lm[[1]]$coef[,1])^2)
for (i in 2:length(mod_fwd)) {mod_fwd_RSS[i]<-sum((Y-cbind(fix_cofs,cof_fwd[[i]])%*%fwd_lm[[i]]$coef[,1])^2)}
mod_bwd_RSS<-vector()
mod_bwd_RSS[1]<-sum((Y-cbind(fix_cofs,cof_bwd[[1]])%*%bwd_lm[[1]]$coef[,1])^2)
for (i in 2:length(mod_bwd)) {mod_bwd_RSS[i]<-sum((Y-cbind(fix_cofs,cof_bwd[[i]])%*%bwd_lm[[i]]$coef[,1])^2)}
expl_RSS<-c(1-sapply(mod_fwd_RSS,function(x){x/RSS_null}),1-sapply(mod_bwd_RSS,function(x){x/RSS_null}))
fix_cofs_RSS<-rep(expl_RSS[1],length(expl_RSS))
cofs_RSS<-expl_RSS-fix_cofs_RSS
h2_RSS<-c(unlist(herit_fwd),unlist(herit_bwd))*(1-expl_RSS)
unexpl_RSS<-1-expl_RSS-h2_RSS
plot_RSS<-t(apply(cbind(fix_cofs_RSS,cofs_RSS,h2_RSS,unexpl_RSS),1,cumsum))
#GLS pvals at each step
pval_step<-list()
pval_step[[1]]<-list(out=data.frame('SNP'=names(pval[[2]]),'pval'=pval[[2]]),cof=addcof_fwd[[1]], "coef"=fwd_lm[[1]]$coef)
for (i in 2:(length(mod_fwd))) {
pval_step[[i]]<-list('out'=rbind(data.frame('SNP'=colnames(cof_fwd[[i]]),'pval'=fwd_lm[[i]]$coef[(ncol(fix_cofs)+1):(ncol(fix_cofs)+ncol(cof_fwd[[i]])),4]),
data.frame('SNP'=names(pval[[i+1]]),'pval'=pval[[i+1]])),
'cof'=colnames(cof_fwd[[i]]),
'coef'=fwd_lm[[i]]$coef)
}
#GLS pvals for best models according to extBIC and mbonf
opt_extBIC<-fwdbwd_table[which(fwdbwd_table$extBIC==min(fwdbwd_table$extBIC))[1],]
opt_mbonf<-(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),])[which(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),]$ncof==max(fwdbwd_table[which(fwdbwd_table$maxpval<=0.05/m),]$ncof))[1],]
if(! is.null(thresh)){
opt_thresh<-(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),])[which(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),]$ncof==max(fwdbwd_table[which(fwdbwd_table$maxpval<=thresh),]$ncof))[1],]
}
bestmodel_pvals<-function(model) {if(substr(model$step_,start=0,stop=3)=='fwd') {
pval_step[[as.integer(substring(model$step_,first=4))+1]]} else if (substr(model$step_,start=0,stop=3)=='bwd') {
cof<-cof_bwd[[as.integer(substring(model$step_,first=4))+1]]
mixedmod<-emma.REMLE(Y,cbind(fix_cofs,cof),K_norm)
M<-solve(chol(mixedmod$vg*K_norm+mixedmod$ve*diag(n)))
Y_t<-crossprod(M,Y)
cof_t<-crossprod(M,cbind(fix_cofs,cof))
GLS_lm<-summary(lm(Y_t~0+cof_t))
Res_H0<-GLS_lm$residuals
Q_ <- qr.Q(qr(cof_t))
RSS<-list()
for (j in 1:(nbchunks-1)) {
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof)])[,((j-1)*round(m/nbchunks)+1):(j*round(m/nbchunks))])
RSS[[j]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t)}
X_t<-crossprod(M %*% (diag(n)-tcrossprod(Q_,Q_)),(X[,!colnames(X) %in% colnames(cof)])[,((j)*round(m/nbchunks)+1):(m-ncol(cof))])
RSS[[nbchunks]]<-apply(X_t,2,function(x){sum(lsfit(x,Res_H0,intercept = FALSE)$residuals^2)})
rm(X_t,j)
RSSf<-unlist(RSS)
RSS_H0<-sum(Res_H0^2)
df2<-n-df1-ncol(fix_cofs)-ncol(cof)
Ftest<-(rep(RSS_H0,length(RSSf))/RSSf-1)*df2/df1
pval<-pf(Ftest,df1,df2,lower.tail=FALSE)
list('out'=rbind(data.frame(SNP=colnames(cof),'pval'=GLS_lm$coef[(ncol(fix_cofs)+1):(ncol(fix_cofs)+ncol(cof)),4]),
data.frame('SNP'=names(pval),'pval'=pval)),
'cof'=colnames(cof),
'coef'=GLS_lm$coef)} else {cat('error \n')}}
opt_extBIC_out<-bestmodel_pvals(opt_extBIC)
opt_mbonf_out<-bestmodel_pvals(opt_mbonf)
if(! is.null(thresh)){
opt_thresh_out<-bestmodel_pvals(opt_thresh)
}
output <- list(step_table=fwdbwd_table,pval_step=pval_step,RSSout=plot_RSS,bonf_thresh=-log10(0.05/m),opt_extBIC=opt_extBIC_out,opt_mbonf=opt_mbonf_out)
if(! is.null(thresh)){
output$thresh <- -log10(thresh)
output$opt_thresh <- opt_thresh_out
}
return(output)
}
`GAPIT.replaceNaN` <-
function(LL) {
#handler of grids with NaN log
#Authors: Zhiwu Zhang
# Last update: may 12, 2011
##############################################################################################
#handler of grids with NaN log
index=(LL=="NaN")
if(length(index)>0) theMin=min(LL[!index])
if(length(index)<1) theMin="NaN"
LL[index]=theMin
return(LL)
}
#=============================================================================================
`GAPIT2` <-
function(Y=NULL,G=NULL,GD=NULL,GM=NULL,KI=NULL,Z=NULL,CV=NULL,CV.Inheritance=NULL,GP=NULL,GK=NULL,
group.from=1000000 ,group.to=1000000,group.by=10,DPP=100000,
kinship.cluster="average", kinship.group='Mean',kinship.algorithm="VanRaden",
bin.from=10000,bin.to=10000,bin.by=10000,inclosure.from=10,inclosure.to=10,inclosure.by=10,
SNP.P3D=TRUE,SNP.effect="Add",SNP.impute="Middle",PCA.total=0, PCA.col=NULL,PCA.3d=FALSE,
SNP.fraction = 1, seed = 123, BINS = 20,SNP.test=TRUE,
SNP.MAF=0,FDR.Rate = 1, SNP.FDR=1,SNP.permutation=FALSE,SNP.CV=NULL,SNP.robust="GLM",
file.from=1, file.to=1, file.total=NULL, file.fragment = 99999,file.path=NULL,
file.G=NULL, file.Ext.G=NULL,file.GD=NULL, file.GM=NULL, file.Ext.GD=NULL,file.Ext.GM=NULL,
ngrid = 100, llim = -10, ulim = 10, esp = 1e-10,
LD.chromosome=NULL,LD.location=NULL,LD.range=NULL,
sangwich.top=NULL,sangwich.bottom=NULL,QC=TRUE,GTindex=NULL,LD=0.1,
NJtree.group=NULL,NJtree.type=c("fan","unrooted"),plot.bin=10^5,
file.output=TRUE,cutOff=0.01, Model.selection = FALSE,output.numerical = FALSE,
output.hapmap = FALSE, Create.indicator = FALSE,
QTN=NULL, QTN.round=1,QTN.limit=0, QTN.update=TRUE, QTN.method="Penalty", Major.allele.zero = FALSE,
method.GLM="fast.lm",method.sub="reward",method.sub.final="reward",method.bin="static",
bin.size=c(1000000),bin.selection=c(10,20,50,100,200,500,1000),
memo="",Prior=NULL,ncpus=1,maxLoop=3,threshold.output=.01,
WS=c(1e0,1e3,1e4,1e5,1e6,1e7),alpha=c(.01,.05,.1,.2,.3,.4,.5,.6,.7,.8,.9,1),maxOut=100,QTN.position=NULL,CG=NULL,
converge=1,iteration.output=FALSE,acceleration=0,iteration.method="accum",PCA.View.output=TRUE,Geno.View.output=TRUE,
plot.style="Oceanic",SUPER_GD=NULL,SUPER_GS=FALSE){
#Object: To perform GWAS and GPS (Genomic Prediction/Selection)
#Designed by Zhiwu Zhang
#Writen by Alex Lipka, Feng Tian ,You Tang and Zhiwu Zhang
#Last update: Oct 23, 2015 by Jiabo Wang add REML threshold and SUPER GK
##############################################################################################
print("--------------------- Welcome to GAPIT ----------------------------")
echo=TRUE
#GAPIT.Version=GAPIT.0000()
Timmer=GAPIT.Timmer(Infor="GAPIT")
Memory=GAPIT.Memory(Infor="GAPIT")
#Genotype processing and calculation Kin and PC
#First call to genotype to setup genotype data
storage_PCA.total<-PCA.total
#if(PCA.total>0){
#if(PCA.total<=3){PCA.total=4}
#}
#BUS algorithm
#if(kinship.algorithm=="FARM-CPU") return (GAPIT.BUS(Y=Y,GDP=GD,GM=GM,CV=CV,
# method.GLM=method.GLM,method.sub=method.sub,method.sub.final=method.sub.final,method.bin=method.bin,
# bin.size=bin.size,bin.selection=bin.selection,file.output=file.output,
# cutOff=cutOff,DPP=DPP,memo=memo,Prior=Prior,ncpus=ncpus,maxLoop=maxLoop,
# kinship.algorithm=kinship.algorithm,GP=GP,threshold.output=threshold.output,
# WS=WS,alpha=alpha,maxOut=maxOut,QTN.position=QTN.position,converge=converge,
# iteration.output=iteration.output,acceleration=acceleration,iteration.method=iteration.method))
myGenotype<-GAPIT.Genotype(G=G,GD=GD,GM=GM,KI=KI,kinship.algorithm=kinship.algorithm,PCA.total=PCA.total,SNP.fraction=SNP.fraction,SNP.test=SNP.test,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,
file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF=SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,NJtree.group=NJtree.group,NJtree.type=NJtree.type,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,
GP=GP,GK=GK,bin.size=NULL,inclosure.size=NULL, Timmer = Timmer,Memory=Memory,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,GTindex=NULL,file.output=file.output, Create.indicator = Create.indicator, Major.allele.zero = Major.allele.zero,Geno.View.output=Geno.View.output,PCA.col=PCA.col,PCA.3d=PCA.3d)
Timmer=myGenotype$Timmer
Memory=myGenotype$Memory
Timmer=GAPIT.Timmer(Timmer=Timmer,Infor="Genotype for all")
Memory=GAPIT.Memory(Memory=Memory,Infor="Genotype for all")
KI=myGenotype$KI
PC=myGenotype$PC
genoFormat=myGenotype$genoFormat
hasGenotype=myGenotype$hasGenotype
byFile=myGenotype$byFile
fullGD=myGenotype$fullGD
GD=myGenotype$GD
GI=myGenotype$GI
GT=myGenotype$GT
G=myGenotype$G
chor_taxa=myGenotype$chor_taxa
#print(dim(GD))
#print(dim(GI))
rownames(GD)=GT
colnames(GD)=GI[,1]
if(output.numerical) write.table(GD, "GAPIT.Genotype.Numerical.txt", quote = FALSE, sep = "\t", row.names = TRUE,col.names = NA)
if(output.hapmap) write.table(myGenotype$G, "GAPIT.Genotype.hmp.txt", quote = FALSE, sep = "\t", row.names = FALSE,col.names = FALSE)
#In case of null Y and null GP, return genotype only
if(is.null(Y) & is.null(GP)) return (list(GWAS=NULL,GPS=NULL,Pred=NULL,compression=NULL,kinship.optimum=NULL,kinship=myGenotype$KI,PCA=myGenotype$PC,GD=data.frame(cbind(as.data.frame(GT),as.data.frame(GD))),GI=GI,G=myGenotype$G))
#In case of null Y, return genotype only
if(is.null(Y)) return (list(GWAS=NULL,GPS=NULL,Pred=NULL,compression=NULL,kinship.optimum=NULL,kinship=myGenotype$KI,PCA=myGenotype$PC,GD=data.frame(cbind(as.date.frame(GT),as.data.frame(GD))),Gi=GI,G=myGenotype$G))
rm(myGenotype)
gc()
PCA.total<-storage_PCA.total
print("--------------------Processing traits----------------------------------")
if(!is.null(Y)){
print("Phenotype provided!")
if(ncol(Y)<2) stop ("Phenotype should have taxa name and one trait at least. Please correct phenotype file!")
for (trait in 2: ncol(Y)) {
traitname=colnames(Y)[trait]
###Statistical distributions of phenotype
if(!is.null(Y) & file.output)ViewPhenotype<-GAPIT.Phenotype.View(myY=Y[,c(1,trait)],traitname=traitname,memo=memo)
###Correlation between phenotype and principal components
if(!is.null(Y)&!is.null(PC) & file.output & PCA.total>0 & PCA.View.output){
myPPV<-GAPIT.Phenotype.PCA.View(
PC=PC,
myY=Y[,c(1,trait)]
)
}
#print(SNP.fraction)
#print("!!!!")
#print(GT)
print(paste("Processing trait: ",traitname,sep=""))
if(!is.null(memo)) traitname=paste(memo,".",traitname,sep="")
#print("!!!!")
#print(dim(Z))
#print(dim(KI))
#print(group.from)
#print(group.to)
gapitMain <- GAPIT.Main(Y=Y[,c(1,trait)],G=G,GD=GD,GM=GI,KI=KI,Z=Z,CV=CV,CV.Inheritance=CV.Inheritance,GP=GP,GK=GK,SNP.P3D=SNP.P3D,kinship.algorithm=kinship.algorithm,
bin.from=bin.from,bin.to=bin.to,bin.by=bin.by,inclosure.from=inclosure.from,inclosure.to=inclosure.to,inclosure.by=inclosure.by,
group.from=group.from,group.to=group.to,group.by=group.by,kinship.cluster=kinship.cluster,kinship.group=kinship.group,name.of.trait=traitname,
file.path=file.path,file.from=file.from, file.to=file.to, file.total=file.total, file.fragment = file.fragment, file.G=file.G,file.Ext.G=file.Ext.G,file.GD=file.GD, file.GM=file.GM, file.Ext.GD=file.Ext.GD,file.Ext.GM=file.Ext.GM,
SNP.MAF= SNP.MAF,FDR.Rate = FDR.Rate,SNP.FDR=SNP.FDR,SNP.effect=SNP.effect,SNP.impute=SNP.impute,PCA.total=PCA.total,GAPIT.Version=GAPIT.Version,
GT=GT, SNP.fraction = SNP.fraction, seed = seed, BINS = BINS,SNP.test=SNP.test,DPP=DPP, SNP.permutation=SNP.permutation,NJtree.group=NJtree.group,NJtree.type=NJtree.type,plot.bin=plot.bin,
LD.chromosome=LD.chromosome,LD.location=LD.location,LD.range=LD.range,SNP.CV=SNP.CV,SNP.robust=SNP.robust,
genoFormat=genoFormat,hasGenotype=hasGenotype,byFile=byFile,fullGD=fullGD,PC=PC,GI=GI,Timmer = Timmer, Memory = Memory,
sangwich.top=sangwich.top,sangwich.bottom=sangwich.bottom,QC=QC,GTindex=GTindex,LD=LD,file.output=file.output,cutOff=cutOff,
Model.selection = Model.selection, Create.indicator = Create.indicator,
QTN=QTN, QTN.round=QTN.round,QTN.limit=QTN.limit, QTN.update=QTN.update, QTN.method=QTN.method, Major.allele.zero=Major.allele.zero,
QTN.position=QTN.position,plot.style=plot.style,SUPER_GS=SUPER_GS,CG=CG,chor_taxa=chor_taxa)
}# end of loop on trait
if(ncol(Y>2) &file.output)
{
Timmer=gapitMain$Timmer
Memory=gapitMain$Memory
file=paste("GAPIT.", "All",".Timming.csv" ,sep = "")
write.table(Timmer, file, quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
file=paste("GAPIT.", "All",".Memory.Stage.csv" ,sep = "")
write.table(Memory, file, quote = FALSE, sep = ",", row.names = FALSE,col.names = TRUE)
}
if(ncol(Y)==2) {
if (!SUPER_GS){
#Evaluate Power vs FDR and type I error
myPower=NULL
if(!is.null(gapitMain$GWAS))myPower=GAPIT.Power(WS=WS, alpha=alpha, maxOut=maxOut,seqQTN=QTN.position,GM=GM,GWAS=gapitMain$GWAS)
h2= as.matrix(as.numeric(as.vector(gapitMain$Compression[,5]))/(as.numeric(as.vector(gapitMain$Compression[,5]))+as.numeric(as.vector(gapitMain$Compression[,6]))),length(gapitMain$Compression[,6]),1)
colnames(h2)=c("Heritability")
print("GAPIT accomplished successfully for single trait. Results are saved. GWAS are returned!")
print("It is OK to see this: 'There were 50 or more warnings (use warnings() to see the first 50)'")
return (list(QTN=gapitMain$QTN,GWAS=gapitMain$GWAS,h2=gapitMain$h2,Pred=gapitMain$Pred,compression=as.data.frame(cbind(gapitMain$Compression,h2)),
kinship.optimum=gapitMain$kinship.optimum,kinship=gapitMain$kinship,PCA=gapitMain$PC,
FDR=myPower$FDR,Power=myPower$Power,Power.Alpha=myPower$Power.Alpha,alpha=myPower$alpha,SUPER_GD=gapitMain$SUPER_GD,P=gapitMain$P,effect.snp=gapitMain$effect.snp,effect.cv=gapitMain$effect.cv))
}else{
h2= as.matrix(as.numeric(as.vector(gapitMain$Compression[,5]))/(as.numeric(as.vector(gapitMain$Compression[,5]))+as.numeric(as.vector(gapitMain$Compression[,6]))),length(gapitMain$Compression[,6]),1)
colnames(h2)=c("Heritability")
print("GAPIT accomplished successfully for single trait. Results are saved. GPS are returned!")
print("It is OK to see this: 'There were 50 or more warnings (use warnings() to see the first 50)'")
return (list(QTN=gapitMain$QTN,GWAS=gapitMain$GWAS,h2=gapitMain$h2,Pred=gapitMain$Pred,compression=as.data.frame(cbind(gapitMain$Compression,h2)),
kinship.optimum=gapitMain$kinship.optimum,kinship=gapitMain$kinship,PCA=gapitMain$PC,
SUPER_GD=gapitMain$SUPER_GD,P=gapitMain$P,effect.snp=gapitMain$effect.snp,effect.cv=gapitMain$effect.cv))
}
}else{
print("GAPIT accomplished successfully for multiple traits. Results are saved")
print("It is OK to see this: 'There were 50 or more warnings (use warnings() to see the first 50)'")
return (list(QTN=NULL,GWAS=NULL,h2=NULL,Pred=NULL,compression=NULL,kinship.optimum=NULL,kinship=gapitMain$KI,PCA=gapitMain$PC,P=gapitMain$P,effect.snp=gapitMain$effect.snp,effect.cv=gapitMain$effect.cv))
}
}# end ofdetecting null Y
} #end of GAPIT function
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