Changes
From Statistical Genetics Courses
hist(blupsgenos$BLUP[blupsgenos$combo==21], main="genotype=21", xlab="BLUP")
hist(blupsgenos$BLUP[blupsgenos$combo==22], main="genotype=22", xlab="BLUP")
q()
gcta64 --bfile quantfamdata --blup-snp GCTAblups.indi.blp --out GCTAsnpblups
R
snpblups<-read.table("GCTAsnpblups.snp.blp", header=F)
names(snpblups)=c("SNP","Allele","snpBLUP","snpResidual")
head(snpblups)
res2<-read.table("FLMMresults", header=T)
new2<-data.frame(res2$SNP, res2$Chromosome, res2$Position, res2$Pvalue)
names(new2)<-c("SNP", "CHR", "BP", "P")
head(new2)
mergeblup=merge(snpblups,new2, by="SNP",sort=F)
head(mergeblup)
par(mfrow=c(1,1))
plot(mergeblup$snpBLUP,-log10(mergeblup$P))
