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R/EBTest.R
In EBSeq: An R package for gene and isoform differential expression analysis of RNA-seq data
Defines functions
EBTest
Documented in
EBTest
EBTest <-
function(Data,NgVector=NULL,Conditions, sizeFactors, maxround, Pool=F, NumBin=1000,ApproxVal=10^-10, Alpha=NULL, Beta=NULL,PInput=NULL,RInput=NULL,PoolLower=.25, PoolUpper=.75,Print=T, Qtrm=1,QtrmCut=0)
{
expect_is(sizeFactors, c("numeric","integer"))
expect_is(maxround, c("numeric","integer"))
if(!is.factor(Conditions))Conditions=as.factor(Conditions)
if(is.null(rownames(Data)))stop("Please add gene/isoform names to the data matrix")
if(!is.matrix(Data))stop("The input Data is not a matrix")
if(length(Conditions)!=ncol(Data))stop("The number of conditions is not the same as the number of samples! ")
if(nlevels(Conditions)>2)stop("More than 2 conditions! Please use EBMultiTest() function")
if(nlevels(Conditions)<2)stop("Less than 2 conditions - Please check your input")
if(length(sizeFactors)!=length(Data) & length(sizeFactors)!=ncol(Data))
stop("The number of library size factors is not the same as the number of samples!")
Conditions=as.factor(Conditions)
Vect5End=Vect3End=CI=CIthre=tau=NULL
Dataraw=Data
#Normalized
DataNorm=GetNormalizedMat(Data, sizeFactors)
expect_is(DataNorm, "matrix")
Levels=levels(as.factor(Conditions))
# Dixon Statistics
# library(outliers)
# normalized matrix for each condition
# matC=sapply(1:length(Levels),function(i)DataNorm[,which(Conditions==Levels[i])])
# run dixon test for each isoform within condition
# DixonP=sapply(1:length(matC),function(j)
# apply(DataNorm,1,function(i){
# if(mean(i)==0)out=NA
# else out=dixon.test(i)$p.value
# out}))
QuantileFor0=apply(DataNorm,1,function(i)quantile(i,Qtrm))
AllZeroNames=which(QuantileFor0<=QtrmCut)
NotAllZeroNames=which(QuantileFor0>QtrmCut)
if(length(AllZeroNames)>0 & Print==T)
cat(paste0("Removing transcripts with ",Qtrm*100,
" th quantile < = ",QtrmCut," \n",
length(NotAllZeroNames)," transcripts will be tested\n"))
if(length(NotAllZeroNames)==0)stop("0 transcript passed")
Data=Data[NotAllZeroNames,]
if(!is.null(NgVector))NgVector=NgVector[NotAllZeroNames]
if(length(sizeFactors)!=ncol(Data))sizeFactors=sizeFactors[NotAllZeroNames,]
if(is.null(NgVector))NgVector=rep(1,nrow(Data))
#Rename Them
IsoNamesIn=rownames(Data)
Names=paste("I",c(1:dim(Data)[1]),sep="")
names(IsoNamesIn)=Names
rownames(Data)=paste("I",c(1:dim(Data)[1]),sep="")
names(NgVector)=paste("I",c(1:dim(Data)[1]),sep="")
if(length(sizeFactors)==length(Data)){
rownames(sizeFactors)=rownames(Data)
colnames(sizeFactors)=Conditions
}
NumOfNg=nlevels(as.factor(NgVector))
NameList=sapply(1:NumOfNg,function(i)Names[NgVector==i],simplify=F)
names(NameList)=paste("Ng",c(1:NumOfNg),sep="")
NotNone=NULL
for (i in 1:NumOfNg) {
if (length(NameList[[i]])!=0)
NotNone=c(NotNone,names(NameList)[i])
}
NameList=NameList[NotNone]
NoneZeroLength=length(NameList)
DataList=vector("list",NoneZeroLength)
DataList=sapply(1:NoneZeroLength , function(i) Data[NameList[[i]],],simplify=F)
names(DataList)=names(NameList)
NumEachGroup=sapply(1:NoneZeroLength , function(i)dim(DataList[[i]])[1])
# Unlist
DataList.unlist=do.call(rbind, DataList)
# Divide by SampleSize factor
if(length(sizeFactors)==ncol(Data))
DataList.unlist.dvd=t(t( DataList.unlist)/sizeFactors)
if(length(sizeFactors)==length(Data))
DataList.unlist.dvd=DataList.unlist/sizeFactors
MeanList=rowMeans(DataList.unlist.dvd)
###############
# Input R
###############
if (!is.null(RInput)){
RNoZero=RInput[NotAllZeroNames]
names(RNoZero)=rownames(Data)
RNoZero.order=RNoZero[rownames(DataList.unlist)]
if(length(sizeFactors)==ncol(Data)){
RMat= outer(RNoZero.order, sizeFactors)
}
if(length(sizeFactors)==length(Data)){
RMat= RNoZero.order* sizeFactors
}
DataListSP=vector("list",nlevels(Conditions))
RMatSP=vector("list",nlevels(Conditions))
for (lv in 1:nlevels(Conditions)){
DataListSP[[lv]]= matrix(DataList.unlist[,Conditions==levels(Conditions)[lv]],nrow=dim(DataList.unlist)[1])
rownames(DataListSP[[lv]])=rownames(DataList.unlist)
RMatSP[[lv]]= matrix(RMat[,Conditions==levels(Conditions)[lv]],nrow=dim(RMat)[1])
rownames(RMatSP[[lv]])=rownames(RMat)
}
F0Log=f0(Input=DataList.unlist, AlphaIn=Alpha, BetaIn=Beta,
EmpiricalR=RMat, NumOfGroups=NumEachGroup, log=T)
F1Log=f1(Input1=DataListSP[[1]], Input2=DataListSP[[2]],
AlphaIn=Alpha, BetaIn=Beta, EmpiricalRSP1=RMatSP[[1]],
EmpiricalRSP2=RMatSP[[2]], NumOfGroup=NumEachGroup, log=T)
F0LogMdf=F0Log+600
F1LogMdf=F1Log+600
F0Mdf=exp(F0LogMdf)
F1Mdf=exp(F1LogMdf)
if(!is.null(PInput)){
z.list=PInput*F1Mdf/(PInput*F1Mdf+(1-PInput)*F0Mdf)
PIn=PInput
}
if(is.null(PInput)){
PIn=.5
PInput=rep(NULL,maxround)
for(i in 1:maxround){
z.list=PIn*F1Mdf/(PIn*F1Mdf+(1-PIn)*F0Mdf)
zNaNName=names(z.list)[is.na(z.list)]
zGood=which(!is.na(z.list))
PIn=sum(z.list[zGood])/length(z.list[zGood])
PInput[i]=PIn
}
zNaNName=names(z.list)[is.na(z.list)]
if(length(zNaNName)!=0){
PNotIn=rep(1-ApproxVal,length(zNaNName))
MeanList.NotIn=MeanList[zNaNName]
R.NotIn.raw=MeanList.NotIn*PNotIn/(1-PNotIn)
if(length(sizeFactors)==ncol(Data))
R.NotIn=outer(R.NotIn.raw,sizeFactors)
if(length(sizeFactors)==length(Data))
R.NotIn=R.NotIn.raw*sizeFactors[zNaNName,]
R.NotIn1=matrix(R.NotIn[,Conditions==levels(Conditions)[1]],nrow=nrow(R.NotIn))
R.NotIn2=matrix(R.NotIn[,Conditions==levels(Conditions)[2]],nrow=nrow(R.NotIn))
NumOfEachGroupNA=sapply(1:NoneZeroLength, function(i)sum(zNaNName%in%rownames(DataList[[i]])))
F0LogNA=f0(matrix(DataList.unlist[zNaNName,],ncol=ncol(DataList.unlist)), Alpha, Beta, R.NotIn, NumOfEachGroupNA, log=T)
F1LogNA=f1(matrix(DataListSP[[1]][zNaNName,],ncol=ncol(DataListSP[[1]])),
matrix(DataListSP[[2]][zNaNName,],ncol=ncol(DataListSP[[2]])),
Alpha, Beta, R.NotIn1,R.NotIn2, NumOfEachGroupNA, log=T)
F0LogMdfNA=F0LogNA+600
F1LogMdfNA=F1LogNA+600
F0MdfNA=exp(F0LogMdfNA)
F1MdfNA=exp(F1LogMdfNA)
z.list.NotIn=PIn*F1MdfNA/(PIn*F1MdfNA+(1-PIn)*F0MdfNA)
z.list[zNaNName]=z.list.NotIn
F0Log[zNaNName]=F0LogNA
F1Log[zNaNName]=F1LogNA
}
}
RealName.Z.output=z.list
RealName.F0=F0Log
RealName.F1=F1Log
names(RealName.Z.output)=IsoNamesIn
names(RealName.F0)=IsoNamesIn
names(RealName.F1)=IsoNamesIn
output=list(Alpha=Alpha,Beta=Beta,P=PInput, Z=RealName.Z.output,
PPDE=RealName.Z.output,f0=RealName.F0, f1=RealName.F1)
return(output)
}
# Get FC and VarPool for pooling - Only works on 2 conditions
if(ncol(Data)==2){
DataforPoolSP.dvd1=matrix(DataList.unlist.dvd[,Conditions==levels(Conditions)[1]],nrow=dim(DataList.unlist)[1])
DataforPoolSP.dvd2=matrix(DataList.unlist.dvd[,Conditions==levels(Conditions)[2]],nrow=dim(DataList.unlist)[1])
MeanforPoolSP.dvd1=rowMeans(DataforPoolSP.dvd1)
MeanforPoolSP.dvd2=rowMeans(DataforPoolSP.dvd2)
FCforPool=MeanforPoolSP.dvd1/MeanforPoolSP.dvd2
names(FCforPool)=rownames(Data)
FC_Use=which(FCforPool>=quantile(FCforPool[!is.na(FCforPool)],PoolLower) &
FCforPool<=quantile(FCforPool[!is.na(FCforPool)],PoolUpper))
Var_FC_Use=apply( DataList.unlist.dvd[FC_Use,],1,var )
Mean_FC_Use=(MeanforPoolSP.dvd1[FC_Use]+MeanforPoolSP.dvd2[FC_Use])/2
MeanforPool=(MeanforPoolSP.dvd1+MeanforPoolSP.dvd2)/2
FC_Use2=which(Var_FC_Use>=Mean_FC_Use)
Var_FC_Use2=Var_FC_Use[FC_Use2]
Mean_FC_Use2=Mean_FC_Use[FC_Use2]
Phi=mean((Var_FC_Use2-Mean_FC_Use2)/Mean_FC_Use2^2)
VarEst= MeanforPool*(1+MeanforPool*Phi)
if(Print==T)message(paste("No Replicate - estimate phi",round(Phi,5), "\n"))
names(VarEst)=names(MeanforPoolSP.dvd1)=
names(MeanforPoolSP.dvd2)=rownames(DataList.unlist.dvd)
}
#DataListSP Here also unlist.. Only two lists
DataListSP=vector("list",nlevels(Conditions))
DataListSP.dvd=vector("list",nlevels(Conditions))
SizeFSP=DataListSP
MeanSP=DataListSP
VarSP=DataListSP
GetPSP=DataListSP
RSP=DataListSP
CISP=DataListSP
tauSP=DataListSP
NumSampleEachCon=rep(NULL,nlevels(Conditions))
for (lv in 1:nlevels(Conditions)){
DataListSP[[lv]]= matrix(DataList.unlist[,Conditions==levels(Conditions)[lv]],nrow=dim(DataList.unlist)[1])
rownames(DataListSP[[lv]])=rownames(DataList.unlist)
DataListSP.dvd[[lv]]= matrix(DataList.unlist.dvd[,Conditions==levels(Conditions)[lv]],nrow=dim(DataList.unlist.dvd)[1])
NumSampleEachCon[lv]=ncol(DataListSP[[lv]])
if(ncol(DataListSP[[lv]])==1 & !is.null(CI)){
CISP[[lv]]=matrix(CI[,Conditions==levels(Conditions)[lv]],nrow=dim(DataList.unlist.dvd)[1])
tauSP[[lv]]=matrix(tau[,Conditions==levels(Conditions)[lv]],nrow=dim(DataList.unlist.dvd)[1])
}
# no matter sizeFactors is a vector or a matrix. Matrix should be columns are the normalization factors
# may input one for each
if(length(sizeFactors)==ncol(Data))SizeFSP[[lv]]=sizeFactors[Conditions==levels(Conditions)[lv]]
if(length(sizeFactors)==length(Data))SizeFSP[[lv]]=sizeFactors[,Conditions==levels(Conditions)[lv]]
MeanSP[[lv]]=rowMeans(DataListSP.dvd[[lv]])
names(MeanSP[[lv]])=rownames(DataListSP[[lv]])
if(length(sizeFactors)==ncol(Data))PrePareVar=sapply(1:ncol( DataListSP[[lv]]),function(i)( DataListSP[[lv]][,i]- SizeFSP[[lv]][i]*MeanSP[[lv]])^2 /SizeFSP[[lv]][i])
if(length(sizeFactors)==length(Data))PrePareVar=sapply(1:ncol( DataListSP[[lv]]),function(i)( DataListSP[[lv]][,i]- SizeFSP[[lv]][,i]*MeanSP[[lv]])^2 /SizeFSP[[lv]][,i])
if(ncol(DataListSP[[lv]])==1 & !is.null(CI))
VarSP[[lv]]=as.vector(((DataListSP[[lv]]/tauSP[[lv]]) * CISP[[lv]]/(CIthre*2))^2)
if(ncol(DataListSP[[lv]])!=1){
VarSP[[lv]]=rowSums(PrePareVar)/ncol( DataListSP[[lv]])
names(MeanSP[[lv]])=rownames(DataList.unlist)
names(VarSP[[lv]])=rownames(DataList.unlist)
GetPSP[[lv]]=MeanSP[[lv]]/VarSP[[lv]]
RSP[[lv]]=MeanSP[[lv]]*GetPSP[[lv]]/(1-GetPSP[[lv]])
}
}
VarList=apply(DataList.unlist.dvd, 1, var)
if(ncol(Data)==2){
PoolVar=VarEst
VarSP[[1]]=VarSP[[2]]=VarEst
GetPSP[[1]]=MeanSP[[1]]/VarEst
GetPSP[[2]]=MeanSP[[2]]/VarEst
}
if(!ncol(Data)==2){
CondWithRep=which(NumSampleEachCon>1)
VarCondWithRep=do.call(cbind,VarSP[CondWithRep])
PoolVar=rowMeans(VarCondWithRep)
}
GetP=MeanList/PoolVar
EmpiricalRList=MeanList*GetP/(1-GetP)
EmpiricalRList[EmpiricalRList==Inf] =max(EmpiricalRList[EmpiricalRList!=Inf])
#####################
if(ncol(Data)!=2){
Varcbind=do.call(cbind,VarSP)
VarrowMin=apply(Varcbind,1,min)
}
if(ncol(Data)==2){
Varcbind=VarEst
VarrowMin=VarEst
VarSP[[1]]=VarSP[[2]]=VarEst
names(MeanSP[[1]])=names(VarSP[[1]])
names(MeanSP[[2]])=names(VarSP[[2]])
}
#
#
GoodData=names(MeanList)[EmpiricalRList>0 & VarrowMin!=0 & EmpiricalRList!=Inf & !is.na(VarrowMin) & !is.na(EmpiricalRList)]
NotIn=names(MeanList)[EmpiricalRList<=0 | VarrowMin==0 | EmpiricalRList==Inf | is.na(VarrowMin) | is.na(EmpiricalRList)]
#print(paste("ZeroVar",sum(VarrowMin==0), "InfR", length(which(EmpiricalRList==Inf)), "Poi", length(which(EmpiricalRList<0)), ""))
EmpiricalRList.NotIn=EmpiricalRList[NotIn]
EmpiricalRList.Good=EmpiricalRList[GoodData]
EmpiricalRList.Good[EmpiricalRList.Good<1]=1+EmpiricalRList.Good[EmpiricalRList.Good<1]
if(length(sizeFactors)==ncol(Data)){
EmpiricalRList.Good.mat= outer(EmpiricalRList.Good, sizeFactors)
EmpiricalRList.mat= outer(EmpiricalRList, sizeFactors)
}
if(length(sizeFactors)==length(Data)){
EmpiricalRList.Good.mat=EmpiricalRList.Good* sizeFactors[GoodData,]
EmpiricalRList.mat=EmpiricalRList* sizeFactors
}
# Only Use Data has Good q's
DataList.In=sapply(1:NoneZeroLength, function(i)DataList[[i]][GoodData[GoodData%in%rownames(DataList[[i]])],],simplify=F)
DataList.NotIn=sapply(1:NoneZeroLength, function(i)DataList[[i]][NotIn[NotIn%in%rownames(DataList[[i]])],],simplify=F)
DataListIn.unlist=do.call(rbind, DataList.In)
DataListNotIn.unlist=do.call(rbind, DataList.NotIn)
DataListSPIn=vector("list",nlevels(Conditions))
DataListSPNotIn=vector("list",nlevels(Conditions))
EmpiricalRList.Good.mat.SP=EmpiricalRList.mat.SP=vector("list",nlevels(Conditions))
for (lv in 1:nlevels(Conditions)){
DataListSPIn[[lv]]= matrix(DataListIn.unlist[,Conditions==levels(Conditions)[lv]],nrow=dim(DataListIn.unlist)[1])
if(length(NotIn)>0){
DataListSPNotIn[[lv]]= matrix(DataListNotIn.unlist[,Conditions==levels(Conditions)[lv]],nrow=dim(DataListNotIn.unlist)[1])
rownames(DataListSPNotIn[[lv]])=rownames(DataListNotIn.unlist)
}
rownames(DataListSPIn[[lv]])=rownames(DataListIn.unlist)
EmpiricalRList.Good.mat.SP[[lv]]=matrix(EmpiricalRList.Good.mat[,Conditions==levels(Conditions)[lv]],nrow=dim(EmpiricalRList.Good.mat)[1])
EmpiricalRList.mat.SP[[lv]]=matrix(EmpiricalRList.mat[,Conditions==levels(Conditions)[lv]],nrow=dim(EmpiricalRList.mat)[1])
}
NumOfEachGroupIn=sapply(1:NoneZeroLength, function(i)max(0,dim(DataList.In[[i]])[1]))
NumOfEachGroupNotIn=sapply(1:NoneZeroLength, function(i)max(0,dim(DataList.NotIn[[i]])[1]))
#################
# For output
#################
RealName.EmpiricalRList=sapply(1:NoneZeroLength,function(i)EmpiricalRList[names(EmpiricalRList)%in%NameList[[i]]], simplify=F)
RealName.MeanList=sapply(1:NoneZeroLength,function(i)MeanList[names(MeanList)%in%NameList[[i]]], simplify=F)
RealName.C1MeanList=sapply(1:NoneZeroLength,function(i)MeanSP[[1]][names(MeanSP[[1]])%in%NameList[[i]]], simplify=F)
RealName.C2MeanList=sapply(1:NoneZeroLength,function(i)MeanSP[[2]][names(MeanSP[[2]])%in%NameList[[i]]], simplify=F)
RealName.C1VarList=sapply(1:NoneZeroLength,function(i)VarSP[[1]][names(VarSP[[1]])%in%NameList[[i]]], simplify=F)
RealName.C2VarList=sapply(1:NoneZeroLength,function(i)VarSP[[2]][names(VarSP[[2]])%in%NameList[[i]]], simplify=F)
RealName.DataList=sapply(1:NoneZeroLength,function(i)DataList[[i]][rownames(DataList[[i]])%in%NameList[[i]],], simplify=F)
RealName.VarList=sapply(1:NoneZeroLength,function(i)VarList[names(VarList)%in%NameList[[i]]], simplify=F)
RealName.PoolVarList=sapply(1:NoneZeroLength,function(i)PoolVar[names(PoolVar)%in%NameList[[i]]], simplify=F)
RealName.QList1=sapply(1:NoneZeroLength,function(i)GetPSP[[1]][names(GetPSP[[1]])%in%NameList[[i]]], simplify=F)
RealName.QList2=sapply(1:NoneZeroLength,function(i)GetPSP[[2]][names(GetPSP[[2]])%in%NameList[[i]]], simplify=F)
if(is.null(unlist(RealName.QList1)))RealName.QList1=RealName.QList2
if(is.null(unlist(RealName.QList2)))RealName.QList2=RealName.QList1
if(is.null(unlist(RealName.C1VarList)))RealName.C1VarList=RealName.C2VarList
if(is.null(unlist(RealName.C2VarList)))RealName.C2VarList=RealName.C1VarList
#browser()
for (i in 1:NoneZeroLength){
tmp=NameList[[i]]
names=IsoNamesIn[tmp]
RealName.MeanList[[i]]=RealName.MeanList[[i]][NameList[[i]]]
RealName.VarList[[i]]=RealName.VarList[[i]][NameList[[i]]]
RealName.QList1[[i]]=RealName.QList1[[i]][NameList[[i]]]
RealName.QList2[[i]]=RealName.QList2[[i]][NameList[[i]]]
RealName.EmpiricalRList[[i]]=RealName.EmpiricalRList[[i]][NameList[[i]]]
RealName.C1MeanList[[i]]=RealName.C1MeanList[[i]][NameList[[i]]]
RealName.C2MeanList[[i]]=RealName.C2MeanList[[i]][NameList[[i]]]
RealName.PoolVarList[[i]]=RealName.PoolVarList[[i]][NameList[[i]]]
RealName.C1VarList[[i]]=RealName.C1VarList[[i]][NameList[[i]]]
RealName.C2VarList[[i]]=RealName.C2VarList[[i]][NameList[[i]]]
RealName.DataList[[i]]=RealName.DataList[[i]][NameList[[i]],]
names(RealName.MeanList[[i]])=names
names(RealName.VarList[[i]])=names
if(ncol(DataListSP[[1]])!=1){
names(RealName.QList1[[i]])=names
names(RealName.C1VarList[[i]])=names
}
if(ncol(DataListSP[[2]])!=1){
names(RealName.QList2[[i]])=names
names(RealName.C2VarList[[i]])=names
}
names(RealName.EmpiricalRList[[i]])=names
names(RealName.C1MeanList[[i]])=names
names(RealName.C2MeanList[[i]])=names
names(RealName.PoolVarList[[i]])=names
rownames(RealName.DataList[[i]])=names
}
#####################
# If Don need EM
#####################
if(!is.null(Alpha)&!is.null(Beta)){
F0Log=f0(Input=DataList.unlist, AlphaIn=Alpha, BetaIn=Beta,
EmpiricalR=EmpiricalRList.mat, NumOfGroups=NumEachGroup, log=T)
F1Log=f1(Input1=DataListSP[[1]], Input2=DataListSP[[2]],
AlphaIn=Alpha, BetaIn=Beta, EmpiricalRSP1=EmpiricalRList.mat.SP[[1]],
EmpiricalRSP2=EmpiricalRList.mat.SP[[2]], NumOfGroup=NumEachGroup, log=T)
F0LogMdf=F0Log+600
F1LogMdf=F1Log+600
F0Mdf=exp(F0LogMdf)
F1Mdf=exp(F1LogMdf)
if(!is.null(PInput)){
z.list=PInput*F1Mdf/(PInput*F1Mdf+(1-PInput)*F0Mdf)
PIn=PInput
}
if(is.null(PInput)){
PIn=.5
PInput=rep(NULL,maxround)
for(i in 1:maxround){
z.list=PIn*F1Mdf/(PIn*F1Mdf+(1-PIn)*F0Mdf)
zNaNName=names(z.list)[is.na(z.list)]
zGood=which(!is.na(z.list))
PIn=sum(z.list[zGood])/length(z.list[zGood])
PInput[i]=PIn
}
zNaNName=names(z.list)[is.na(z.list)]
if(length(zNaNName)!=0){
PNotIn=rep(1-ApproxVal,length(zNaNName))
MeanList.NotIn=MeanList[zNaNName]
R.NotIn.raw=MeanList.NotIn*PNotIn/(1-PNotIn)
if(length(sizeFactors)==ncol(Data))
R.NotIn=outer(R.NotIn.raw,sizeFactors)
if(length(sizeFactors)==length(Data))
R.NotIn=R.NotIn.raw*sizeFactors[zNaNName,]
R.NotIn1=matrix(R.NotIn[,Conditions==levels(Conditions)[1]],nrow=nrow(R.NotIn))
R.NotIn2=matrix(R.NotIn[,Conditions==levels(Conditions)[2]],nrow=nrow(R.NotIn))
NumOfEachGroupNA=sapply(1:NoneZeroLength, function(i)sum(zNaNName%in%rownames(DataList[[i]])))
F0LogNA=f0(matrix(DataList.unlist[zNaNName,], ncol=ncol(DataList.unlist)), Alpha, Beta, R.NotIn, NumOfEachGroupNA, log=T)
F1LogNA=f1(matrix(DataListSP[[1]][zNaNName,],ncol=ncol(DataListSP[[1]])),
matrix(DataListSP[[2]][zNaNName,],ncol=ncol(DataListSP[[2]])),
Alpha, Beta, R.NotIn1,R.NotIn2, NumOfEachGroupNA, log=T)
F0LogMdfNA=F0LogNA+600
F1LogMdfNA=F1LogNA+600
F0MdfNA=exp(F0LogMdfNA)
F1MdfNA=exp(F1LogMdfNA)
z.list.NotIn=PIn*F1MdfNA/(PIn*F1MdfNA+(1-PIn)*F0MdfNA)
z.list[zNaNName]=z.list.NotIn
F0Log[zNaNName]=F0LogNA
F1Log[zNaNName]=F1LogNA
}
}
RealName.Z.output=z.list
RealName.F0=F0Log
RealName.F1=F1Log
names(RealName.Z.output)=IsoNamesIn
names(RealName.F0)=IsoNamesIn
names(RealName.F1)=IsoNamesIn
output=list(Alpha=Alpha,Beta=Beta,P=PInput, Z=RealName.Z.output,
RList=RealName.EmpiricalRList, MeanList=RealName.MeanList,
VarList=RealName.VarList, QList1=RealName.QList1, QList2=RealName.QList2,
C1Mean=RealName.C1MeanList, C2Mean=RealName.C2MeanList,
C1EstVar=RealName.C1VarList, C2EstVar=RealName.C2VarList,
PoolVar=RealName.PoolVarList , DataList=RealName.DataList,
PPDE=RealName.Z.output,f0=RealName.F0, f1=RealName.F1)
return(output)
}
#####################
#Initialize SigIn & ...
#####################
AlphaIn=0.5
BetaIn=rep(0.5,NoneZeroLength)
PIn=0.5
#####################
# EM
#####################
UpdateAlpha=NULL
UpdateBeta=NULL
UpdateP=NULL
UpdatePFromZ=NULL
Timeperround=NULL
for (times in 1:maxround){
temptime1=proc.time()
UpdateOutput=suppressWarnings(LogN(DataListIn.unlist,DataListSPIn, EmpiricalRList.Good.mat ,EmpiricalRList.Good.mat.SP, NumOfEachGroupIn, AlphaIn, BetaIn, PIn, NoneZeroLength))
message(paste("iteration", times, "done \n",sep=" "))
AlphaIn=UpdateOutput$AlphaNew
BetaIn=UpdateOutput$BetaNew
PIn=UpdateOutput$PNew
PFromZ=UpdateOutput$PFromZ
F0Out=UpdateOutput$F0Out
F1Out=UpdateOutput$F1Out
UpdateAlpha=rbind(UpdateAlpha,AlphaIn)
UpdateBeta=rbind(UpdateBeta,BetaIn)
UpdateP=rbind(UpdateP,PIn)
UpdatePFromZ=rbind(UpdatePFromZ,PFromZ)
temptime2=proc.time()
Timeperround=c(Timeperround,temptime2[3]-temptime1[3])
message(paste("time" ,round(Timeperround[times],2),"\n",sep=" "))
Z.output=UpdateOutput$ZNew.list[!is.na(UpdateOutput$ZNew.list)]
Z.NA.Names=UpdateOutput$zNaNName
}
#Remove this } after testing!!
# if (times!=1){
# if((UpdateAlpha[times]-UpdateAlpha[times-1])^2+UpdateBeta[times]-UpdateBeta[times-1])^2+UpdateR[times]-UpdateR[times-1])^2+UpdateP[times]-UpdateP[times-1])^2<=10^(-6)){
# Result=list(Sig=SigIn, Miu=MiuIn, Tau=TauIn)
# break
# }
# }
#}
##########Change Names############
## Only z are for Good Ones
GoodData=GoodData[!GoodData%in%Z.NA.Names]
IsoNamesIn.Good=IsoNamesIn[GoodData]
RealName.Z.output=Z.output
RealName.F0=F0Out
RealName.F1=F1Out
names(RealName.Z.output)=IsoNamesIn.Good
names(RealName.F0)=IsoNamesIn.Good
names(RealName.F1)=IsoNamesIn.Good
#########posterior part for other data set here later############
AllNA=unique(c(Z.NA.Names,NotIn))
z.list.NotIn=NULL
AllF0=c(RealName.F0)
AllF1=c(RealName.F1)
AllZ=RealName.Z.output
if (length(AllNA)>0){
Ng.NA=NgVector[AllNA]
AllNA.Ngorder=AllNA[order(Ng.NA)]
NumOfEachGroupNA=rep(0,NoneZeroLength)
NumOfEachGroupNA.tmp=tapply(Ng.NA,Ng.NA,length)
names(NumOfEachGroupNA)=c(1:NoneZeroLength)
NumOfEachGroupNA[names(NumOfEachGroupNA.tmp)]=NumOfEachGroupNA.tmp
PNotIn=rep(1-ApproxVal,length(AllNA.Ngorder))
MeanList.NotIn=MeanList[AllNA.Ngorder]
R.NotIn.raw=MeanList.NotIn*PNotIn/(1-PNotIn)
if(length(sizeFactors)==ncol(Data))
R.NotIn=outer(R.NotIn.raw,sizeFactors)
if(length(sizeFactors)==length(Data))
R.NotIn=R.NotIn.raw*sizeFactors[names(R.NotIn.raw),]
R.NotIn1=matrix(R.NotIn[,Conditions==levels(Conditions)[1]],nrow=nrow(R.NotIn))
R.NotIn2=matrix(R.NotIn[,Conditions==levels(Conditions)[2]],nrow=nrow(R.NotIn))
DataListNotIn.unlistWithZ=matrix(DataList.unlist[AllNA.Ngorder,],nrow=length(AllNA.Ngorder))
DataListSPNotInWithZ=vector("list",nlevels(Conditions))
for (lv in 1:nlevels(Conditions))
DataListSPNotInWithZ[[lv]] = matrix(DataListSP[[lv]][AllNA.Ngorder,],nrow=length(AllNA.Ngorder))
F0Log=f0(DataListNotIn.unlistWithZ, AlphaIn, BetaIn, R.NotIn, NumOfEachGroupNA, log=T)
F1Log=f1(DataListSPNotInWithZ[[1]], DataListSPNotInWithZ[[2]], AlphaIn, BetaIn, R.NotIn1,R.NotIn2, NumOfEachGroupNA, log=T)
F0LogMdf=F0Log+600
F1LogMdf=F1Log+600
F0Mdf=exp(F0LogMdf)
F1Mdf=exp(F1LogMdf)
z.list.NotIn=PIn*F1Mdf/(PIn*F1Mdf+(1-PIn)*F0Mdf)
# names(z.list.NotIn)=IsoNamesIn.Good=IsoNamesIn[which(Names%in%NotIn)]
names(z.list.NotIn)=IsoNamesIn[AllNA.Ngorder]
AllZ=c(RealName.Z.output,z.list.NotIn)
AllZ=AllZ[IsoNamesIn]
AllZ[is.na(AllZ)]=0
F0.NotIn=F0Log
F1.NotIn=F1Log
names(F0.NotIn)=IsoNamesIn[names(F0Log)]
names(F1.NotIn)=IsoNamesIn[names(F1Log)]
AllF0=c(RealName.F0,F0.NotIn)
AllF1=c(RealName.F1,F1.NotIn)
AllF0=AllF0[IsoNamesIn]
AllF1=AllF1[IsoNamesIn]
AllF0[is.na(AllF0)]=0
AllF1[is.na(AllF1)]=0
}
PPMatNZ=cbind(1-AllZ,AllZ)
colnames(PPMatNZ)=c("PPEE","PPDE")
rownames(UpdateAlpha)=paste("iter",1:nrow(UpdateAlpha),sep="")
rownames(UpdateBeta)=paste("iter",1:nrow(UpdateBeta),sep="")
rownames(UpdateP)=paste("iter",1:nrow(UpdateP),sep="")
rownames(UpdatePFromZ)=paste("iter",1:nrow(UpdatePFromZ),sep="")
colnames(UpdateBeta)=paste("Ng",1:ncol(UpdateBeta),sep="")
CondOut=levels(Conditions)
names(CondOut)=paste("Condition",c(1:length(CondOut)),sep="")
PPMat=matrix(NA,ncol=2,nrow=nrow(Dataraw))
rownames(PPMat)=rownames(Dataraw)
colnames(PPMat)=c("PPEE","PPDE")
if(is.null(AllZeroNames))PPMat=PPMatNZ
if(!is.null(AllZeroNames))PPMat[names(NotAllZeroNames),]=PPMatNZ[names(NotAllZeroNames),]
#############Result############################
Result=list(Alpha=UpdateAlpha,Beta=UpdateBeta,P=UpdateP,
PFromZ=UpdatePFromZ, Z=RealName.Z.output,PoissonZ=z.list.NotIn,
RList=RealName.EmpiricalRList, MeanList=RealName.MeanList,
VarList=RealName.VarList, QList1=RealName.QList1, QList2=RealName.QList2,
C1Mean=RealName.C1MeanList, C2Mean=RealName.C2MeanList,C1EstVar=RealName.C1VarList,
C2EstVar=RealName.C2VarList, PoolVar=RealName.PoolVarList ,
DataList=RealName.DataList,PPDE=AllZ,f0=AllF0, f1=AllF1,
AllZeroIndex=AllZeroNames,PPMat=PPMatNZ, PPMatWith0=PPMat,
ConditionOrder=CondOut, Conditions=Conditions, DataNorm=DataNorm)
}
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Defines functions EBTest
Documented in EBTest
EBTest <-
function(Data,NgVector=NULL,Conditions, sizeFactors, maxround, Pool=F, NumBin=1000,ApproxVal=10^-10, Alpha=NULL, Beta=NULL,PInput=NULL,RInput=NULL,PoolLower=.25, PoolUpper=.75,Print=T, Qtrm=1,QtrmCut=0)
{
expect_is(sizeFactors, c("numeric","integer"))
expect_is(maxround, c("numeric","integer"))
if(!is.factor(Conditions))Conditions=as.factor(Conditions)
if(is.null(rownames(Data)))stop("Please add gene/isoform names to the data matrix")
if(!is.matrix(Data))stop("The input Data is not a matrix")
if(length(Conditions)!=ncol(Data))stop("The number of conditions is not the same as the number of samples! ")
if(nlevels(Conditions)>2)stop("More than 2 conditions! Please use EBMultiTest() function")
if(nlevels(Conditions)<2)stop("Less than 2 conditions - Please check your input")
if(length(sizeFactors)!=length(Data) & length(sizeFactors)!=ncol(Data))
stop("The number of library size factors is not the same as the number of samples!")
Conditions=as.factor(Conditions)
Vect5End=Vect3End=CI=CIthre=tau=NULL
Dataraw=Data
#Normalized
DataNorm=GetNormalizedMat(Data, sizeFactors)
expect_is(DataNorm, "matrix")
Levels=levels(as.factor(Conditions))
# Dixon Statistics
# library(outliers)
# normalized matrix for each condition
# matC=sapply(1:length(Levels),function(i)DataNorm[,which(Conditions==Levels[i])])
# run dixon test for each isoform within condition
# DixonP=sapply(1:length(matC),function(j)
# apply(DataNorm,1,function(i){
# if(mean(i)==0)out=NA
# else out=dixon.test(i)$p.value
# out}))
QuantileFor0=apply(DataNorm,1,function(i)quantile(i,Qtrm))
AllZeroNames=which(QuantileFor0<=QtrmCut)
NotAllZeroNames=which(QuantileFor0>QtrmCut)
if(length(AllZeroNames)>0 & Print==T)
cat(paste0("Removing transcripts with ",Qtrm*100,
" th quantile < = ",QtrmCut," \n",
length(NotAllZeroNames)," transcripts will be tested\n"))
if(length(NotAllZeroNames)==0)stop("0 transcript passed")
Data=Data[NotAllZeroNames,]
if(!is.null(NgVector))NgVector=NgVector[NotAllZeroNames]
if(length(sizeFactors)!=ncol(Data))sizeFactors=sizeFactors[NotAllZeroNames,]
if(is.null(NgVector))NgVector=rep(1,nrow(Data))
#Rename Them
IsoNamesIn=rownames(Data)
Names=paste("I",c(1:dim(Data)[1]),sep="")
names(IsoNamesIn)=Names
rownames(Data)=paste("I",c(1:dim(Data)[1]),sep="")
names(NgVector)=paste("I",c(1:dim(Data)[1]),sep="")
if(length(sizeFactors)==length(Data)){
rownames(sizeFactors)=rownames(Data)
colnames(sizeFactors)=Conditions
}
NumOfNg=nlevels(as.factor(NgVector))
NameList=sapply(1:NumOfNg,function(i)Names[NgVector==i],simplify=F)
names(NameList)=paste("Ng",c(1:NumOfNg),sep="")
NotNone=NULL
for (i in 1:NumOfNg) {
if (length(NameList[[i]])!=0)
NotNone=c(NotNone,names(NameList)[i])
}
NameList=NameList[NotNone]
NoneZeroLength=length(NameList)
DataList=vector("list",NoneZeroLength)
DataList=sapply(1:NoneZeroLength , function(i) Data[NameList[[i]],],simplify=F)
names(DataList)=names(NameList)
NumEachGroup=sapply(1:NoneZeroLength , function(i)dim(DataList[[i]])[1])
# Unlist
DataList.unlist=do.call(rbind, DataList)
# Divide by SampleSize factor
if(length(sizeFactors)==ncol(Data))
DataList.unlist.dvd=t(t( DataList.unlist)/sizeFactors)
if(length(sizeFactors)==length(Data))
DataList.unlist.dvd=DataList.unlist/sizeFactors
MeanList=rowMeans(DataList.unlist.dvd)
###############
# Input R
###############
if (!is.null(RInput)){
RNoZero=RInput[NotAllZeroNames]
names(RNoZero)=rownames(Data)
RNoZero.order=RNoZero[rownames(DataList.unlist)]
if(length(sizeFactors)==ncol(Data)){
RMat= outer(RNoZero.order, sizeFactors)
}
if(length(sizeFactors)==length(Data)){
RMat= RNoZero.order* sizeFactors
}
DataListSP=vector("list",nlevels(Conditions))
RMatSP=vector("list",nlevels(Conditions))
for (lv in 1:nlevels(Conditions)){
DataListSP[[lv]]= matrix(DataList.unlist[,Conditions==levels(Conditions)[lv]],nrow=dim(DataList.unlist)[1])
rownames(DataListSP[[lv]])=rownames(DataList.unlist)
RMatSP[[lv]]= matrix(RMat[,Conditions==levels(Conditions)[lv]],nrow=dim(RMat)[1])
rownames(RMatSP[[lv]])=rownames(RMat)
}
F0Log=f0(Input=DataList.unlist, AlphaIn=Alpha, BetaIn=Beta,
EmpiricalR=RMat, NumOfGroups=NumEachGroup, log=T)
F1Log=f1(Input1=DataListSP[[1]], Input2=DataListSP[[2]],
AlphaIn=Alpha, BetaIn=Beta, EmpiricalRSP1=RMatSP[[1]],
EmpiricalRSP2=RMatSP[[2]], NumOfGroup=NumEachGroup, log=T)
F0LogMdf=F0Log+600
F1LogMdf=F1Log+600
F0Mdf=exp(F0LogMdf)
F1Mdf=exp(F1LogMdf)
if(!is.null(PInput)){
z.list=PInput*F1Mdf/(PInput*F1Mdf+(1-PInput)*F0Mdf)
PIn=PInput
}
if(is.null(PInput)){
PIn=.5
PInput=rep(NULL,maxround)
for(i in 1:maxround){
z.list=PIn*F1Mdf/(PIn*F1Mdf+(1-PIn)*F0Mdf)
zNaNName=names(z.list)[is.na(z.list)]
zGood=which(!is.na(z.list))
PIn=sum(z.list[zGood])/length(z.list[zGood])
PInput[i]=PIn
}
zNaNName=names(z.list)[is.na(z.list)]
if(length(zNaNName)!=0){
PNotIn=rep(1-ApproxVal,length(zNaNName))
MeanList.NotIn=MeanList[zNaNName]
R.NotIn.raw=MeanList.NotIn*PNotIn/(1-PNotIn)
if(length(sizeFactors)==ncol(Data))
R.NotIn=outer(R.NotIn.raw,sizeFactors)
if(length(sizeFactors)==length(Data))
R.NotIn=R.NotIn.raw*sizeFactors[zNaNName,]
R.NotIn1=matrix(R.NotIn[,Conditions==levels(Conditions)[1]],nrow=nrow(R.NotIn))
R.NotIn2=matrix(R.NotIn[,Conditions==levels(Conditions)[2]],nrow=nrow(R.NotIn))
NumOfEachGroupNA=sapply(1:NoneZeroLength, function(i)sum(zNaNName%in%rownames(DataList[[i]])))
F0LogNA=f0(matrix(DataList.unlist[zNaNName,],ncol=ncol(DataList.unlist)), Alpha, Beta, R.NotIn, NumOfEachGroupNA, log=T)
F1LogNA=f1(matrix(DataListSP[[1]][zNaNName,],ncol=ncol(DataListSP[[1]])),
matrix(DataListSP[[2]][zNaNName,],ncol=ncol(DataListSP[[2]])),
Alpha, Beta, R.NotIn1,R.NotIn2, NumOfEachGroupNA, log=T)
F0LogMdfNA=F0LogNA+600
F1LogMdfNA=F1LogNA+600
F0MdfNA=exp(F0LogMdfNA)
F1MdfNA=exp(F1LogMdfNA)
z.list.NotIn=PIn*F1MdfNA/(PIn*F1MdfNA+(1-PIn)*F0MdfNA)
z.list[zNaNName]=z.list.NotIn
F0Log[zNaNName]=F0LogNA
F1Log[zNaNName]=F1LogNA
}
}
RealName.Z.output=z.list
RealName.F0=F0Log
RealName.F1=F1Log
names(RealName.Z.output)=IsoNamesIn
names(RealName.F0)=IsoNamesIn
names(RealName.F1)=IsoNamesIn
output=list(Alpha=Alpha,Beta=Beta,P=PInput, Z=RealName.Z.output,
PPDE=RealName.Z.output,f0=RealName.F0, f1=RealName.F1)
return(output)
}
# Get FC and VarPool for pooling - Only works on 2 conditions
if(ncol(Data)==2){
DataforPoolSP.dvd1=matrix(DataList.unlist.dvd[,Conditions==levels(Conditions)[1]],nrow=dim(DataList.unlist)[1])
DataforPoolSP.dvd2=matrix(DataList.unlist.dvd[,Conditions==levels(Conditions)[2]],nrow=dim(DataList.unlist)[1])
MeanforPoolSP.dvd1=rowMeans(DataforPoolSP.dvd1)
MeanforPoolSP.dvd2=rowMeans(DataforPoolSP.dvd2)
FCforPool=MeanforPoolSP.dvd1/MeanforPoolSP.dvd2
names(FCforPool)=rownames(Data)
FC_Use=which(FCforPool>=quantile(FCforPool[!is.na(FCforPool)],PoolLower) &
FCforPool<=quantile(FCforPool[!is.na(FCforPool)],PoolUpper))
Var_FC_Use=apply( DataList.unlist.dvd[FC_Use,],1,var )
Mean_FC_Use=(MeanforPoolSP.dvd1[FC_Use]+MeanforPoolSP.dvd2[FC_Use])/2
MeanforPool=(MeanforPoolSP.dvd1+MeanforPoolSP.dvd2)/2
FC_Use2=which(Var_FC_Use>=Mean_FC_Use)
Var_FC_Use2=Var_FC_Use[FC_Use2]
Mean_FC_Use2=Mean_FC_Use[FC_Use2]
Phi=mean((Var_FC_Use2-Mean_FC_Use2)/Mean_FC_Use2^2)
VarEst= MeanforPool*(1+MeanforPool*Phi)
if(Print==T)message(paste("No Replicate - estimate phi",round(Phi,5), "\n"))
names(VarEst)=names(MeanforPoolSP.dvd1)=
names(MeanforPoolSP.dvd2)=rownames(DataList.unlist.dvd)
}
#DataListSP Here also unlist.. Only two lists
DataListSP=vector("list",nlevels(Conditions))
DataListSP.dvd=vector("list",nlevels(Conditions))
SizeFSP=DataListSP
MeanSP=DataListSP
VarSP=DataListSP
GetPSP=DataListSP
RSP=DataListSP
CISP=DataListSP
tauSP=DataListSP
NumSampleEachCon=rep(NULL,nlevels(Conditions))
for (lv in 1:nlevels(Conditions)){
DataListSP[[lv]]= matrix(DataList.unlist[,Conditions==levels(Conditions)[lv]],nrow=dim(DataList.unlist)[1])
rownames(DataListSP[[lv]])=rownames(DataList.unlist)
DataListSP.dvd[[lv]]= matrix(DataList.unlist.dvd[,Conditions==levels(Conditions)[lv]],nrow=dim(DataList.unlist.dvd)[1])
NumSampleEachCon[lv]=ncol(DataListSP[[lv]])
if(ncol(DataListSP[[lv]])==1 & !is.null(CI)){
CISP[[lv]]=matrix(CI[,Conditions==levels(Conditions)[lv]],nrow=dim(DataList.unlist.dvd)[1])
tauSP[[lv]]=matrix(tau[,Conditions==levels(Conditions)[lv]],nrow=dim(DataList.unlist.dvd)[1])
}
# no matter sizeFactors is a vector or a matrix. Matrix should be columns are the normalization factors
# may input one for each
if(length(sizeFactors)==ncol(Data))SizeFSP[[lv]]=sizeFactors[Conditions==levels(Conditions)[lv]]
if(length(sizeFactors)==length(Data))SizeFSP[[lv]]=sizeFactors[,Conditions==levels(Conditions)[lv]]
MeanSP[[lv]]=rowMeans(DataListSP.dvd[[lv]])
names(MeanSP[[lv]])=rownames(DataListSP[[lv]])
if(length(sizeFactors)==ncol(Data))PrePareVar=sapply(1:ncol( DataListSP[[lv]]),function(i)( DataListSP[[lv]][,i]- SizeFSP[[lv]][i]*MeanSP[[lv]])^2 /SizeFSP[[lv]][i])
if(length(sizeFactors)==length(Data))PrePareVar=sapply(1:ncol( DataListSP[[lv]]),function(i)( DataListSP[[lv]][,i]- SizeFSP[[lv]][,i]*MeanSP[[lv]])^2 /SizeFSP[[lv]][,i])
if(ncol(DataListSP[[lv]])==1 & !is.null(CI))
VarSP[[lv]]=as.vector(((DataListSP[[lv]]/tauSP[[lv]]) * CISP[[lv]]/(CIthre*2))^2)
if(ncol(DataListSP[[lv]])!=1){
VarSP[[lv]]=rowSums(PrePareVar)/ncol( DataListSP[[lv]])
names(MeanSP[[lv]])=rownames(DataList.unlist)
names(VarSP[[lv]])=rownames(DataList.unlist)
GetPSP[[lv]]=MeanSP[[lv]]/VarSP[[lv]]
RSP[[lv]]=MeanSP[[lv]]*GetPSP[[lv]]/(1-GetPSP[[lv]])
}
}
VarList=apply(DataList.unlist.dvd, 1, var)
if(ncol(Data)==2){
PoolVar=VarEst
VarSP[[1]]=VarSP[[2]]=VarEst
GetPSP[[1]]=MeanSP[[1]]/VarEst
GetPSP[[2]]=MeanSP[[2]]/VarEst
}
if(!ncol(Data)==2){
CondWithRep=which(NumSampleEachCon>1)
VarCondWithRep=do.call(cbind,VarSP[CondWithRep])
PoolVar=rowMeans(VarCondWithRep)
}
GetP=MeanList/PoolVar
EmpiricalRList=MeanList*GetP/(1-GetP)
EmpiricalRList[EmpiricalRList==Inf] =max(EmpiricalRList[EmpiricalRList!=Inf])
#####################
if(ncol(Data)!=2){
Varcbind=do.call(cbind,VarSP)
VarrowMin=apply(Varcbind,1,min)
}
if(ncol(Data)==2){
Varcbind=VarEst
VarrowMin=VarEst
VarSP[[1]]=VarSP[[2]]=VarEst
names(MeanSP[[1]])=names(VarSP[[1]])
names(MeanSP[[2]])=names(VarSP[[2]])
}
#
#
GoodData=names(MeanList)[EmpiricalRList>0 & VarrowMin!=0 & EmpiricalRList!=Inf & !is.na(VarrowMin) & !is.na(EmpiricalRList)]
NotIn=names(MeanList)[EmpiricalRList<=0 | VarrowMin==0 | EmpiricalRList==Inf | is.na(VarrowMin) | is.na(EmpiricalRList)]
#print(paste("ZeroVar",sum(VarrowMin==0), "InfR", length(which(EmpiricalRList==Inf)), "Poi", length(which(EmpiricalRList<0)), ""))
EmpiricalRList.NotIn=EmpiricalRList[NotIn]
EmpiricalRList.Good=EmpiricalRList[GoodData]
EmpiricalRList.Good[EmpiricalRList.Good<1]=1+EmpiricalRList.Good[EmpiricalRList.Good<1]
if(length(sizeFactors)==ncol(Data)){
EmpiricalRList.Good.mat= outer(EmpiricalRList.Good, sizeFactors)
EmpiricalRList.mat= outer(EmpiricalRList, sizeFactors)
}
if(length(sizeFactors)==length(Data)){
EmpiricalRList.Good.mat=EmpiricalRList.Good* sizeFactors[GoodData,]
EmpiricalRList.mat=EmpiricalRList* sizeFactors
}
# Only Use Data has Good q's
DataList.In=sapply(1:NoneZeroLength, function(i)DataList[[i]][GoodData[GoodData%in%rownames(DataList[[i]])],],simplify=F)
DataList.NotIn=sapply(1:NoneZeroLength, function(i)DataList[[i]][NotIn[NotIn%in%rownames(DataList[[i]])],],simplify=F)
DataListIn.unlist=do.call(rbind, DataList.In)
DataListNotIn.unlist=do.call(rbind, DataList.NotIn)
DataListSPIn=vector("list",nlevels(Conditions))
DataListSPNotIn=vector("list",nlevels(Conditions))
EmpiricalRList.Good.mat.SP=EmpiricalRList.mat.SP=vector("list",nlevels(Conditions))
for (lv in 1:nlevels(Conditions)){
DataListSPIn[[lv]]= matrix(DataListIn.unlist[,Conditions==levels(Conditions)[lv]],nrow=dim(DataListIn.unlist)[1])
if(length(NotIn)>0){
DataListSPNotIn[[lv]]= matrix(DataListNotIn.unlist[,Conditions==levels(Conditions)[lv]],nrow=dim(DataListNotIn.unlist)[1])
rownames(DataListSPNotIn[[lv]])=rownames(DataListNotIn.unlist)
}
rownames(DataListSPIn[[lv]])=rownames(DataListIn.unlist)
EmpiricalRList.Good.mat.SP[[lv]]=matrix(EmpiricalRList.Good.mat[,Conditions==levels(Conditions)[lv]],nrow=dim(EmpiricalRList.Good.mat)[1])
EmpiricalRList.mat.SP[[lv]]=matrix(EmpiricalRList.mat[,Conditions==levels(Conditions)[lv]],nrow=dim(EmpiricalRList.mat)[1])
}
NumOfEachGroupIn=sapply(1:NoneZeroLength, function(i)max(0,dim(DataList.In[[i]])[1]))
NumOfEachGroupNotIn=sapply(1:NoneZeroLength, function(i)max(0,dim(DataList.NotIn[[i]])[1]))
#################
# For output
#################
RealName.EmpiricalRList=sapply(1:NoneZeroLength,function(i)EmpiricalRList[names(EmpiricalRList)%in%NameList[[i]]], simplify=F)
RealName.MeanList=sapply(1:NoneZeroLength,function(i)MeanList[names(MeanList)%in%NameList[[i]]], simplify=F)
RealName.C1MeanList=sapply(1:NoneZeroLength,function(i)MeanSP[[1]][names(MeanSP[[1]])%in%NameList[[i]]], simplify=F)
RealName.C2MeanList=sapply(1:NoneZeroLength,function(i)MeanSP[[2]][names(MeanSP[[2]])%in%NameList[[i]]], simplify=F)
RealName.C1VarList=sapply(1:NoneZeroLength,function(i)VarSP[[1]][names(VarSP[[1]])%in%NameList[[i]]], simplify=F)
RealName.C2VarList=sapply(1:NoneZeroLength,function(i)VarSP[[2]][names(VarSP[[2]])%in%NameList[[i]]], simplify=F)
RealName.DataList=sapply(1:NoneZeroLength,function(i)DataList[[i]][rownames(DataList[[i]])%in%NameList[[i]],], simplify=F)
RealName.VarList=sapply(1:NoneZeroLength,function(i)VarList[names(VarList)%in%NameList[[i]]], simplify=F)
RealName.PoolVarList=sapply(1:NoneZeroLength,function(i)PoolVar[names(PoolVar)%in%NameList[[i]]], simplify=F)
RealName.QList1=sapply(1:NoneZeroLength,function(i)GetPSP[[1]][names(GetPSP[[1]])%in%NameList[[i]]], simplify=F)
RealName.QList2=sapply(1:NoneZeroLength,function(i)GetPSP[[2]][names(GetPSP[[2]])%in%NameList[[i]]], simplify=F)
if(is.null(unlist(RealName.QList1)))RealName.QList1=RealName.QList2
if(is.null(unlist(RealName.QList2)))RealName.QList2=RealName.QList1
if(is.null(unlist(RealName.C1VarList)))RealName.C1VarList=RealName.C2VarList
if(is.null(unlist(RealName.C2VarList)))RealName.C2VarList=RealName.C1VarList
#browser()
for (i in 1:NoneZeroLength){
tmp=NameList[[i]]
names=IsoNamesIn[tmp]
RealName.MeanList[[i]]=RealName.MeanList[[i]][NameList[[i]]]
RealName.VarList[[i]]=RealName.VarList[[i]][NameList[[i]]]
RealName.QList1[[i]]=RealName.QList1[[i]][NameList[[i]]]
RealName.QList2[[i]]=RealName.QList2[[i]][NameList[[i]]]
RealName.EmpiricalRList[[i]]=RealName.EmpiricalRList[[i]][NameList[[i]]]
RealName.C1MeanList[[i]]=RealName.C1MeanList[[i]][NameList[[i]]]
RealName.C2MeanList[[i]]=RealName.C2MeanList[[i]][NameList[[i]]]
RealName.PoolVarList[[i]]=RealName.PoolVarList[[i]][NameList[[i]]]
RealName.C1VarList[[i]]=RealName.C1VarList[[i]][NameList[[i]]]
RealName.C2VarList[[i]]=RealName.C2VarList[[i]][NameList[[i]]]
RealName.DataList[[i]]=RealName.DataList[[i]][NameList[[i]],]
names(RealName.MeanList[[i]])=names
names(RealName.VarList[[i]])=names
if(ncol(DataListSP[[1]])!=1){
names(RealName.QList1[[i]])=names
names(RealName.C1VarList[[i]])=names
}
if(ncol(DataListSP[[2]])!=1){
names(RealName.QList2[[i]])=names
names(RealName.C2VarList[[i]])=names
}
names(RealName.EmpiricalRList[[i]])=names
names(RealName.C1MeanList[[i]])=names
names(RealName.C2MeanList[[i]])=names
names(RealName.PoolVarList[[i]])=names
rownames(RealName.DataList[[i]])=names
}
#####################
# If Don need EM
#####################
if(!is.null(Alpha)&!is.null(Beta)){
F0Log=f0(Input=DataList.unlist, AlphaIn=Alpha, BetaIn=Beta,
EmpiricalR=EmpiricalRList.mat, NumOfGroups=NumEachGroup, log=T)
F1Log=f1(Input1=DataListSP[[1]], Input2=DataListSP[[2]],
AlphaIn=Alpha, BetaIn=Beta, EmpiricalRSP1=EmpiricalRList.mat.SP[[1]],
EmpiricalRSP2=EmpiricalRList.mat.SP[[2]], NumOfGroup=NumEachGroup, log=T)
F0LogMdf=F0Log+600
F1LogMdf=F1Log+600
F0Mdf=exp(F0LogMdf)
F1Mdf=exp(F1LogMdf)
if(!is.null(PInput)){
z.list=PInput*F1Mdf/(PInput*F1Mdf+(1-PInput)*F0Mdf)
PIn=PInput
}
if(is.null(PInput)){
PIn=.5
PInput=rep(NULL,maxround)
for(i in 1:maxround){
z.list=PIn*F1Mdf/(PIn*F1Mdf+(1-PIn)*F0Mdf)
zNaNName=names(z.list)[is.na(z.list)]
zGood=which(!is.na(z.list))
PIn=sum(z.list[zGood])/length(z.list[zGood])
PInput[i]=PIn
}
zNaNName=names(z.list)[is.na(z.list)]
if(length(zNaNName)!=0){
PNotIn=rep(1-ApproxVal,length(zNaNName))
MeanList.NotIn=MeanList[zNaNName]
R.NotIn.raw=MeanList.NotIn*PNotIn/(1-PNotIn)
if(length(sizeFactors)==ncol(Data))
R.NotIn=outer(R.NotIn.raw,sizeFactors)
if(length(sizeFactors)==length(Data))
R.NotIn=R.NotIn.raw*sizeFactors[zNaNName,]
R.NotIn1=matrix(R.NotIn[,Conditions==levels(Conditions)[1]],nrow=nrow(R.NotIn))
R.NotIn2=matrix(R.NotIn[,Conditions==levels(Conditions)[2]],nrow=nrow(R.NotIn))
NumOfEachGroupNA=sapply(1:NoneZeroLength, function(i)sum(zNaNName%in%rownames(DataList[[i]])))
F0LogNA=f0(matrix(DataList.unlist[zNaNName,], ncol=ncol(DataList.unlist)), Alpha, Beta, R.NotIn, NumOfEachGroupNA, log=T)
F1LogNA=f1(matrix(DataListSP[[1]][zNaNName,],ncol=ncol(DataListSP[[1]])),
matrix(DataListSP[[2]][zNaNName,],ncol=ncol(DataListSP[[2]])),
Alpha, Beta, R.NotIn1,R.NotIn2, NumOfEachGroupNA, log=T)
F0LogMdfNA=F0LogNA+600
F1LogMdfNA=F1LogNA+600
F0MdfNA=exp(F0LogMdfNA)
F1MdfNA=exp(F1LogMdfNA)
z.list.NotIn=PIn*F1MdfNA/(PIn*F1MdfNA+(1-PIn)*F0MdfNA)
z.list[zNaNName]=z.list.NotIn
F0Log[zNaNName]=F0LogNA
F1Log[zNaNName]=F1LogNA
}
}
RealName.Z.output=z.list
RealName.F0=F0Log
RealName.F1=F1Log
names(RealName.Z.output)=IsoNamesIn
names(RealName.F0)=IsoNamesIn
names(RealName.F1)=IsoNamesIn
output=list(Alpha=Alpha,Beta=Beta,P=PInput, Z=RealName.Z.output,
RList=RealName.EmpiricalRList, MeanList=RealName.MeanList,
VarList=RealName.VarList, QList1=RealName.QList1, QList2=RealName.QList2,
C1Mean=RealName.C1MeanList, C2Mean=RealName.C2MeanList,
C1EstVar=RealName.C1VarList, C2EstVar=RealName.C2VarList,
PoolVar=RealName.PoolVarList , DataList=RealName.DataList,
PPDE=RealName.Z.output,f0=RealName.F0, f1=RealName.F1)
return(output)
}
#####################
#Initialize SigIn & ...
#####################
AlphaIn=0.5
BetaIn=rep(0.5,NoneZeroLength)
PIn=0.5
#####################
# EM
#####################
UpdateAlpha=NULL
UpdateBeta=NULL
UpdateP=NULL
UpdatePFromZ=NULL
Timeperround=NULL
for (times in 1:maxround){
temptime1=proc.time()
UpdateOutput=suppressWarnings(LogN(DataListIn.unlist,DataListSPIn, EmpiricalRList.Good.mat ,EmpiricalRList.Good.mat.SP, NumOfEachGroupIn, AlphaIn, BetaIn, PIn, NoneZeroLength))
message(paste("iteration", times, "done \n",sep=" "))
AlphaIn=UpdateOutput$AlphaNew
BetaIn=UpdateOutput$BetaNew
PIn=UpdateOutput$PNew
PFromZ=UpdateOutput$PFromZ
F0Out=UpdateOutput$F0Out
F1Out=UpdateOutput$F1Out
UpdateAlpha=rbind(UpdateAlpha,AlphaIn)
UpdateBeta=rbind(UpdateBeta,BetaIn)
UpdateP=rbind(UpdateP,PIn)
UpdatePFromZ=rbind(UpdatePFromZ,PFromZ)
temptime2=proc.time()
Timeperround=c(Timeperround,temptime2[3]-temptime1[3])
message(paste("time" ,round(Timeperround[times],2),"\n",sep=" "))
Z.output=UpdateOutput$ZNew.list[!is.na(UpdateOutput$ZNew.list)]
Z.NA.Names=UpdateOutput$zNaNName
}
#Remove this } after testing!!
# if (times!=1){
# if((UpdateAlpha[times]-UpdateAlpha[times-1])^2+UpdateBeta[times]-UpdateBeta[times-1])^2+UpdateR[times]-UpdateR[times-1])^2+UpdateP[times]-UpdateP[times-1])^2<=10^(-6)){
# Result=list(Sig=SigIn, Miu=MiuIn, Tau=TauIn)
# break
# }
# }
#}
##########Change Names############
## Only z are for Good Ones
GoodData=GoodData[!GoodData%in%Z.NA.Names]
IsoNamesIn.Good=IsoNamesIn[GoodData]
RealName.Z.output=Z.output
RealName.F0=F0Out
RealName.F1=F1Out
names(RealName.Z.output)=IsoNamesIn.Good
names(RealName.F0)=IsoNamesIn.Good
names(RealName.F1)=IsoNamesIn.Good
#########posterior part for other data set here later############
AllNA=unique(c(Z.NA.Names,NotIn))
z.list.NotIn=NULL
AllF0=c(RealName.F0)
AllF1=c(RealName.F1)
AllZ=RealName.Z.output
if (length(AllNA)>0){
Ng.NA=NgVector[AllNA]
AllNA.Ngorder=AllNA[order(Ng.NA)]
NumOfEachGroupNA=rep(0,NoneZeroLength)
NumOfEachGroupNA.tmp=tapply(Ng.NA,Ng.NA,length)
names(NumOfEachGroupNA)=c(1:NoneZeroLength)
NumOfEachGroupNA[names(NumOfEachGroupNA.tmp)]=NumOfEachGroupNA.tmp
PNotIn=rep(1-ApproxVal,length(AllNA.Ngorder))
MeanList.NotIn=MeanList[AllNA.Ngorder]
R.NotIn.raw=MeanList.NotIn*PNotIn/(1-PNotIn)
if(length(sizeFactors)==ncol(Data))
R.NotIn=outer(R.NotIn.raw,sizeFactors)
if(length(sizeFactors)==length(Data))
R.NotIn=R.NotIn.raw*sizeFactors[names(R.NotIn.raw),]
R.NotIn1=matrix(R.NotIn[,Conditions==levels(Conditions)[1]],nrow=nrow(R.NotIn))
R.NotIn2=matrix(R.NotIn[,Conditions==levels(Conditions)[2]],nrow=nrow(R.NotIn))
DataListNotIn.unlistWithZ=matrix(DataList.unlist[AllNA.Ngorder,],nrow=length(AllNA.Ngorder))
DataListSPNotInWithZ=vector("list",nlevels(Conditions))
for (lv in 1:nlevels(Conditions))
DataListSPNotInWithZ[[lv]] = matrix(DataListSP[[lv]][AllNA.Ngorder,],nrow=length(AllNA.Ngorder))
F0Log=f0(DataListNotIn.unlistWithZ, AlphaIn, BetaIn, R.NotIn, NumOfEachGroupNA, log=T)
F1Log=f1(DataListSPNotInWithZ[[1]], DataListSPNotInWithZ[[2]], AlphaIn, BetaIn, R.NotIn1,R.NotIn2, NumOfEachGroupNA, log=T)
F0LogMdf=F0Log+600
F1LogMdf=F1Log+600
F0Mdf=exp(F0LogMdf)
F1Mdf=exp(F1LogMdf)
z.list.NotIn=PIn*F1Mdf/(PIn*F1Mdf+(1-PIn)*F0Mdf)
# names(z.list.NotIn)=IsoNamesIn.Good=IsoNamesIn[which(Names%in%NotIn)]
names(z.list.NotIn)=IsoNamesIn[AllNA.Ngorder]
AllZ=c(RealName.Z.output,z.list.NotIn)
AllZ=AllZ[IsoNamesIn]
AllZ[is.na(AllZ)]=0
F0.NotIn=F0Log
F1.NotIn=F1Log
names(F0.NotIn)=IsoNamesIn[names(F0Log)]
names(F1.NotIn)=IsoNamesIn[names(F1Log)]
AllF0=c(RealName.F0,F0.NotIn)
AllF1=c(RealName.F1,F1.NotIn)
AllF0=AllF0[IsoNamesIn]
AllF1=AllF1[IsoNamesIn]
AllF0[is.na(AllF0)]=0
AllF1[is.na(AllF1)]=0
}
PPMatNZ=cbind(1-AllZ,AllZ)
colnames(PPMatNZ)=c("PPEE","PPDE")
rownames(UpdateAlpha)=paste("iter",1:nrow(UpdateAlpha),sep="")
rownames(UpdateBeta)=paste("iter",1:nrow(UpdateBeta),sep="")
rownames(UpdateP)=paste("iter",1:nrow(UpdateP),sep="")
rownames(UpdatePFromZ)=paste("iter",1:nrow(UpdatePFromZ),sep="")
colnames(UpdateBeta)=paste("Ng",1:ncol(UpdateBeta),sep="")
CondOut=levels(Conditions)
names(CondOut)=paste("Condition",c(1:length(CondOut)),sep="")
PPMat=matrix(NA,ncol=2,nrow=nrow(Dataraw))
rownames(PPMat)=rownames(Dataraw)
colnames(PPMat)=c("PPEE","PPDE")
if(is.null(AllZeroNames))PPMat=PPMatNZ
if(!is.null(AllZeroNames))PPMat[names(NotAllZeroNames),]=PPMatNZ[names(NotAllZeroNames),]
#############Result############################
Result=list(Alpha=UpdateAlpha,Beta=UpdateBeta,P=UpdateP,
PFromZ=UpdatePFromZ, Z=RealName.Z.output,PoissonZ=z.list.NotIn,
RList=RealName.EmpiricalRList, MeanList=RealName.MeanList,
VarList=RealName.VarList, QList1=RealName.QList1, QList2=RealName.QList2,
C1Mean=RealName.C1MeanList, C2Mean=RealName.C2MeanList,C1EstVar=RealName.C1VarList,
C2EstVar=RealName.C2VarList, PoolVar=RealName.PoolVarList ,
DataList=RealName.DataList,PPDE=AllZ,f0=AllF0, f1=AllF1,
AllZeroIndex=AllZeroNames,PPMat=PPMatNZ, PPMatWith0=PPMat,
ConditionOrder=CondOut, Conditions=Conditions, DataNorm=DataNorm)
}
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