Changes

==GeneABEL==

plink --file GWAS_clean4 --pheno pheno.phen --pheno-name Aff --transpose --recode --out gwa_gabel

plink --file GWAS_clean4 --pheno pheno.phen --pheno-name systolic --transpose --recode --out gwa_gabel_qtl

plot(test.qt, col = "black")

add.plot(test.eg, col = "gray", pch = 3)

plink --file chr22_imputation_ex<br data-attributes="%20/" />plink --file chr22_imputation_ex --maf 0.01 --mind 0.02 --geno 0.05 --hwe 0.001 --out qc_check<br data-attributes="%20/" />plink --file chr22_imputation_ex --maf 0.01 --mind 0.02 --geno 0.05 --hwe 0.001 --recode --out chr22_clean1<br data-attributes="%20/" />plink --file chr22_clean1 --maf 0.01 --mind 0.02 --geno 0.05 --hwe 0.001 --out qc_check_2<br data-attributes="%20/" />plink --file chr22_clean1 --filter-cases --hwe 0.001 --recode --out chr22_cases_clean<br data-attributes="%20/" />plink --file chr22_clean1 --filter-controls --recode --out chr22_controls_clean<br data-attributes="%20/" />plink --file chr22_controls_clean --merge chr22_cases_clean.ped chr22_cases_clean.map -–hwe 0.001 --recode --out chr22_all_clean<br data-attributes="%20/" />plink --file chr22_all_clean --logistic --out chr22_all_clean_geno<br data-attributes="%20/" />R<br data-attributes="%20/" />mydata = read.table(“chr22_all_clean_geno.assoc.logistic”, header=T)<br data-attributes="%20/" />names(mydata)<br data-attributes="%20/" />plot(mydata$BP, -log10(mydata$P))<br data-attributes="%20/" />smallp = mydata[which(mydata$P < 1E-4),]<br data-attributes="%20/" />smallp<br data-attributes="%20/" />smallp = smallp[order(smallp$BP),]<br data-attributes="%20/" />smallp<br data-attributes="%20/" />q()<br data-attributes="%20/" />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<br data-attributes="%20/" />plink –-dosage chr22_HIHII_dose_mach4plink.txt.gz Zin –-fam chr22_imputation_ex.fam –-map chr22_imputed_snps_positions.map --out chr22_HIHII_dosage<br data-attributes="%20/" />R<br data-attributes="%20/" />dosage = read.table("chr22_HIHII_dosage.assoc.dosage", header= T)<br data-attributes="%20/" />names(dosage)<br data-attributes="%20/" />plot(dosage$BP, -log10(dosage$P))<br data-attributes="%20/" />dosagep = dosage[which(dosage$P < 5E-8),]<br data-attributes="%20/" />dosagep = dosagep[order(dosagep$BP),]<br data-attributes="%20/" />dosagep<br data-attributes="%20/" />interest = dosage[which(dosage$SNP=='rs715586'),]<br data-attributes="%20/" />interest