==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 plink --file chr22_imputation_ex --maf 0.01 --mind 0.02 --geno 0.05 --hwe 0.001 --recode --out chr22_clean1--noweb plink --file chr22_clean1 --maf 0.01 --mind 0.02 --geno 0.05 --hwe 0.001 --out qc_check_2--noweb plink --file chr22_clean1 --filter-cases --hwe 0.001 --recode --out chr22_cases_clean--noweb plink --file chr22_clean1 --filter-controls --recode --out chr22_controls_clean--noweb plink --file chr22_controls_clean --merge chr22_cases_clean.ped chr22_cases_clean.map -–hwe -hwe 0.001 --recode --out chr22_all_clean--noweb plink --file chr22_all_clean --logistic --out chr22_all_clean_geno--noweb
R
mydata = read.table(“chr22_all_clean_geno.assoc.logistic”, header=T)
smallp
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
R
dosage = read.table("chr22_HIHII_dosage.assoc.dosage", header= T)
interest = dosage[which(dosage$SNP=='rs715586'),]
interest
==PLINK_R==