#Create QQ plot using R

read.table("plink.cmh",header=T)->data


#QQ plot based on the expected chisq distribution
qqplot(qchisq((1:length(data$CHISQ))/length(data$CHISQ),1),data$CHISQ,xlim=c(0,25),ylim=c(0,25),xlab="Expected Chi Square",ylab="Observed Chi Square")
abline(0,1)