==Imputation exercise==
plink --file chr22_imputation_ex --noweb
plink --file chr22_imputation_ex --maf 0.01 --mind 0.02 --geno 0.05 --hwe 0.001 --out qc_check --noweb
q()
mach1 --hapmapFormat -d chr22_mach_merlin.map -p chr22_mach_merlin.ped --haps genotypes_chr22_CEU_r22_nr.b36_fwd.phase.gz --snps genotypes_chr22_CEU_r22_nr.b36_fwd_legend.txt.gz --greedy --rounds 100 --mle --mldetails --autoflip -o chr22_HIHII
plink --dosage chr22_HIHII_dose_mach4plink.txt.gz Zin --fam chr22_imputation_ex.fam --map chr22_imputed_snps_positions.map --out chr22_HIHII_dosage--noweb
R
dosage = read.table("chr22_HIHII_dosage.assoc.dosage", header= T)