Nothing
geepack.quant.int.batch.imputed <- function(phenfile,genfile,pedfile,phen,covars,cov.int,sub="N",outfile,col.names=T,sep.ped=",",sep.phe=",",sep.gen=","){
######################check input files, parameters#########
###########################################################
#do not run when 1) no covariates or no cov.int; 2) the length of cov.int is not 1; 3) cov.int is not in covariates
if (sum((!is.na(cov.int))*(sum(is.na(covars))!=1))!=1 | length(cov.int)!=1 | sum(cov.int %in% covars)!=1) stop('one interaction covariate is allowed and it has to be in covariates')
cor.snp <- function(y,x){ #########
if(!is.numeric(y))y<-as.numeric(as.factor(y)) ########
return(sd(y)==0 || abs(cor(y,x,use="complete"))>0.99999999 )} #########
if (sum(is.na(sub))==1) sub <- "N" ####061009
assign("phen", phen, pos=-1,inherits=T)
assign("cov.int", cov.int, pos=-1,inherits=T)
read.in.data <- function(phenfile,genfile,pedfile,sep.ped=sep.ped,sep.phe=sep.phe,sep.gen=sep.gen) {
print("Reading in Data")
ped.dat <- read.table(genfile,header=TRUE,na.strings="",sep=sep.gen)
snp.names <- names(ped.dat)[-1]
pedigree <- read.table(pedfile,header=TRUE,sep=sep.ped)
gntp.all <- merge(pedigree,ped.dat,by="id")
#read in phenotype data
phen.dat=read.table(phenfile,header=TRUE,sep=sep.phe)
phen.name=colnames(phen.dat)[-1]
n.snp=length(names(gntp.all))
if(length(grep("^sex$",colnames(phen.dat)))==0) {
phensnp.dat<-merge(gntp.all,phen.dat,by=c("id"))
} else {
## sex is one of the columns in the phenotype file
phensnp.dat<-merge(gntp.all,phen.dat,by=c("id","sex"))
}
print("Done reading in data")
return(list(data=phensnp.dat,snps=snp.names,phen.name=phen.name))
}
#####################main programs##########################
phensnp.dat <- read.in.data(phenfile,genfile,pedfile,sep.ped=sep.ped,sep.phe=sep.phe,sep.gen=sep.gen)
snplist<-phensnp.dat$snps
if (sum(phensnp.dat$phen.name %in% covars)==length(covars)) phenlist<-phensnp.dat$phen.name[!phensnp.dat$phen.name %in% covars] else #######
stop('some covariates are not available') #######
test.dat <- phensnp.dat$data
test.dat <- test.dat[order(test.dat$famid),]
if (length(table(test.dat[,cov.int]))!=2 & sub=="Y") stop('No subset analysis for non-binary interaction covariate!') ####061009
result <- NULL
if (sum(is.na(covars))==0 & sum(snplist %in% covars)>=1) {
names(test.dat)[which(snplist %in% covars)+6] <- snplist[snplist %in% covars]
covars[covars %in% snplist] <- paste(covars[covars %in% snplist],".y",sep="")
}
cov.int.snp <- NA #100708
if (sum(is.na(cov.int))==0 & sum(snplist %in% cov.int)==1) {
cov.int.snp <- snplist[snplist %in% cov.int]
cov.int <- paste(cov.int,".y",sep="")
} #100708
idlab="famid"
for (i in snplist) {
test2.dat <- na.omit(test.dat[,c(i,phen,idlab,covars)]) #######
x.covar<-as.matrix(test2.dat[,covars])
famid <- test2.dat[,idlab] ####### 5)
bin.flag <- length(table(test2.dat[,cov.int]))
snp <- test2.dat[,i]
if (bin.flag==2) bin <- sort(as.numeric(names(table(test2.dat[,cov.int]))))
if (length(covars)>1) colinear <- apply(x.covar,2,cor.snp,x=test2.dat[,i]) else colinear <- cor.snp(x.covar,test2.dat[,i]) #######
x.int<-test2.dat[,cov.int]*snp; #######071409
colinear <- c(colinear,cor.snp(snp,x.int),cor.snp(test2.dat[,cov.int],x.int)) #######071409
imaf <- mean(test2.dat[,i])/2
count<-table(snp)
count1 <- c(0,0)
count1[1] <- length(test2.dat[,i])
count1[2] <- imaf
testiMAF <- 2*count1[1]*imaf*(1-imaf)
if (bin.flag<2) result<-rbind(result,c(phen,i,cov.int,count1[1:2],rep(NA,8))) else {
if (length(count)==1 | sum(colinear,na.rm=T)>0 | length(unique(snp))==1 || testiMAF <= 1 | length(unique(x.int))==1){
if (bin.flag>2) result<-rbind(result,c(phen,i,cov.int,count1[1:2],rep(NA,8))) else {
if (sub=="Y") result<-rbind(result,c(phen,i,cov.int,count1[1:2],rep(NA,13))) else result<-rbind(result,c(phen,i,cov.int,count1[1:2],rep(NA,8)))} #061009
} else {
if (bin.flag>2) {
gee.test.v <- try(geese(test2.dat[,phen]~snp+x.int+x.covar,id=famid,corstr="independence"))
if (!"try-error" %in% class(gee.test.v) & gee.test.v$error==0) {
gee.test <- summary(gee.test.v)
tmp <- c(gee.test.v$vbeta[names(gee.test.v$beta)=="snp",names(gee.test.v$beta)=="x.int"],"additive",unlist(gee.test$mean["snp",1:2]),
pchisq(gee.test$mean["snp",3],1,lower.tail=F),unlist(gee.test$mean["x.int",1:2]),pchisq(gee.test$mean["x.int",3],1,lower.tail=F))
} else tmp <- c(rep(NA,8))
} else {
if (sub=="Y") { #061009
#tab1 <- table(x.covar[x.covar[,cov.int]==bin[1],cov.int],snp[x.covar[,cov.int]==bin[1]]) ######05132009 imputed.X
#tab2 <- table(x.covar[x.covar[,cov.int]==bin[2],cov.int],snp[x.covar[,cov.int]==bin[2]])
#if (length(tab1)==1 | length(tab2)==1) tmp <- c(rep(NA,13)) else { ######05132009 imputed.X
if (sum(!covars %in% cov.int)>0) { ####replace !covar %in% cov.int
xcovar.bin<-as.matrix(test2.dat[,covars[!covars %in% cov.int]])
gee.test1 <- try(summary(geese(test2.dat[,phen]~snp+xcovar.bin,id=famid,corstr="independence",subset=test2.dat[,cov.int]==bin[1])))
gee.test2 <- try(summary(geese(test2.dat[,phen]~snp+xcovar.bin,id=famid,corstr="independence",subset=test2.dat[,cov.int]==bin[2])))
gee.test <- try(summary(geese(test2.dat[,phen]~snp+x.int+x.covar,id=famid,corstr="independence")))
} else {
gee.test1 <- try(summary(geese(test2.dat[,phen]~snp,id=famid,corstr="independence",subset=test2.dat[,cov.int]==bin[1])))
gee.test2 <- try(summary(geese(test2.dat[,phen]~snp,id=famid,corstr="independence",subset=test2.dat[,cov.int]==bin[2])))
gee.test <- try(summary(geese(test2.dat[,phen]~snp+x.int+x.covar,id=famid,corstr="independence")))
}
if (sum(c(class(gee.test1),class(gee.test2),class(gee.test))=="try-error")==0 & sum(c(gee.test$error,gee.test1$error,gee.test2$error))==0) { ###061209
tmp <- c("additive",unlist(gee.test$mean["snp",1:2]),pchisq(gee.test$mean["snp",3],1,lower.tail=F),unlist(gee.test1$mean["snp",1:2]),
pchisq(gee.test1$mean["snp",3],1,lower.tail=F),unlist(gee.test2$mean["snp",1:2]),pchisq(gee.test2$mean["snp",3],1,lower.tail=F),
unlist(gee.test$mean["x.int",1:2]),pchisq(gee.test$mean["x.int",3],1,lower.tail=F))
} else {
if ("try-error" %in% c(class(gee.test1),class(gee.test2)) & !"try-error" %in% class(gee.test) & gee.test$error==0 & sum(c(gee.test1$error,gee.test2$error))!=0) {
tmp <- c("additive",unlist(gee.test$mean["snp",1:2]),pchisq(gee.test$mean["snp",3],1,lower.tail=F),rep(NA,6),unlist(gee.test$mean["x.int",1:2]),
pchisq(gee.test$mean["x.int",3],1,lower.tail=F))
} else tmp <- c(rep(NA,13))
#}
}
} else {
gee.test.v <- try(geese(test2.dat[,phen]~snp+x.int+x.covar,id=famid,corstr="independence"))
if (!"try-error" %in% class(gee.test.v) & gee.test.v$error==0) {
gee.test <- summary(gee.test.v)
tmp <- c(gee.test.v$vbeta[names(gee.test.v$beta)=="snp",names(gee.test.v$beta)=="x.int"],"additive",unlist(gee.test$mean["snp",1:2]),
pchisq(gee.test$mean["snp",3],1,lower.tail=F),unlist(gee.test$mean["x.int",1:2]),pchisq(gee.test$mean["x.int",3],1,lower.tail=F))
} else tmp <- c(rep(NA,8))
}
}
if (bin.flag>2) result<-rbind(result, c(phen,i,cov.int,count1[1:2],tmp)) else {
if (sub=="Y") result<-rbind(result,c(phen,i,cov.int,count1[1:2],tmp)) else result<-rbind(result,c(phen,i,cov.int,count1[1:2],tmp))} #061009
}
}
}
if (length(table(test.dat[,cov.int]))>2) colnames(result)<-c("phen","snp","covar_int","n","AF","cov_beta_snp_beta_int","model","beta_snp","se_snp","pval_snp","beta_int","se_int","pval_int") else {
if (sub=="Y") colnames(result)<-c("phen","snp","covar_int","n","AF","model","beta_snp","se_snp","pval_snp","beta_snp_cov0","se_snp_cov0","pval_snp_cov0","beta_snp_cov1","se_snp_cov1","pval_snp_cov1","beta_int","se_int","pval_int") else
colnames(result)<-c("phen","snp","covar_int","n","AF","cov_beta_snp_beta_int","model","beta_snp","se_snp","pval_snp","beta_int","se_int","pval_int")}
if (sum(is.na(cov.int.snp))==0 & length(cov.int.snp)==1) { #100708
result[,"covar_int"] <- cov.int.snp
} #100708
write.table(result, outfile, quote=F,row.names=F, col.names=T,sep=",",na="",append=T)
}
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