myvars = c("FID1", "IID1", "FID2", "IID2", "PI_HAT")
problem_pairs[myvars]
plink --file GWAS_clean3 --pheno pheno.txt --pheno-name Aff --hardy
q()
plink --file GWAS_clean2 --remove IBS_excluded.txt --recode --out GWAS_clean3
plink --file GWAS_clean3 --pheno pheno.txt --pheno-name Aff --hardy
R
hardy = read.table("plink.hwe", header = T)
names(hardy)
hwe_prob = hardy[which(hardy$P < 0.0000009),]
hwe_prob
q()
plink --file GWAS_clean3 --exclude HWE_out.txt --recode --out GWAS_clean4