==GeneABEL==
plink --file GWAS_clean4 --pheno pheno.phen --pheno-name Aff --transpose --recode --out gwa_gabel --noweb
plink --file GWAS_clean4 --pheno pheno.phen --pheno-name systolic --transpose --recode --out gwa_gabel_qtl --noweb
descriptives.scan(test.eg)
snp.eg <- row.names(results(test.eg))[results(test.eg)$P1df < alpha]
pvalue.eg <- results(test.eg)$P1df[results(test.eg)$P1df < alpha] lambda.eg <- test.eg@lambda snp.eg pvalue.eg
lambda.eg
for (k in 1:10){
plot(test.qt, col = "black")
add.plot(test.eg, col = "gray", pch = 3)
legend("topright", c("Original plot","After correction w/ EIGENSTRAT"), pch = c(1,3))==GWAS Data QC==
==GWAS Data QC==
plink --file GWAS --noweb
plink --file GWAS --mind 0.10 --recode --out GWAS_clean_mind --noweb
gws_adjusted
q()
==VAT==
vtools -h
vtools init VATDemo