Family-based Association Exercise
From Statistical Genetics Courses
Family-based Association Exercise
cd exercises/cordell/FASTLMM_GCTA ls -l plink --bfile quantfamdata --assoc --out plinkresults R res1<-read.table("plinkresults.qassoc", header=T) head(res1) source("qqmanHJCupdated.R") manhattan(res1, pch=20, suggestiveline=F, genomewideline=F, ymin=2, cex.x.axis=0.65, colors=c("black","dodgerblue"), cex=0.5) qq(res1$P) chi<-(qchisq(1-res1$P,1)) lambda=median(chi)/0.456 lambda fastlmmc -bfile quantfamdata -pheno quantfamdata.fam -mpheno 4 -bfileSim quantfamdata -ML -out FLMMresults R res2<-read.table("FLMMresults", header=T) head(res2) chi<-(qchisq(1-res2$Pvalue,1)) lambda=median(chi)/0.456 lambda new<-data.frame(res2$SNP, res2$Chromosome, res2$Position, res2$Pvalue) names(new)<-c("SNP", "CHR", "BP", "P") head(new) qq(new$P) manhattan(new, pch=20, suggestiveline=F, genomewideline=F, ymin=2, cex.x.axis=0.65, colors=c("black","dodgerblue"), cex=0.5)
