==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
R
library(GenABEL)
cps <- cps.full$points
plot(cps[,1], cps[,2], pch = g.dat@phdata$popn)
legend(”topright”"topright", c("TSI","MEX", "CEU"), pch = c(1,2,3))
colnames(cps)<-c('C1','C2','C3','C4','C5','C6','C7','C8','C9','C10')
gpc.dat <- g.dat