Gender.R

dataFile<-commandArgs()[6]
resultFile<-commandArgs()[7]

#gender
d1=read.table(dataFile, header=T,as.is=T)
#table(d1[,1:2])
if (length(which(d1$PEDSEX==1 | d1$PEDSEX==2))<=3) {
	cat(paste("There are not enough male(1) or female(2) in PEDSEX of file ",dataFile,"; Will not generate the figure\n",sep=""))
} else {
	male=subset(d1, d1$PEDSEX==1)
	female=subset(d1, d1$PEDSEX==2)
	jpeg(resultFile, res=300, width=10, height=5, units="in")
	par(mfcol=c(1,2), pty="m")
	hist(male[,6], main="Male", ylab="Freq", xlab="Chr X inbreeding estimate", breaks =100)
	hist(female[,6], main="Female", ylab="Freq", xlab="Chr X inbreeding estimate", breaks=100)
	result<-dev.off()
	cat(paste(resultFile," was successfully generated.\n",sep=""))
}