plink --file GWAS_clean3 --exclude HWE_out.txt --recode --out GWAS_clean4 --noweb
MultifactorialPart 1
plink --ped dbp.cc.ped --map dbp.map --map3 --out logreg.add --logistic --noweb
plink --ped dbp.cc.ped --map dbp.map --map3 --out logreg.snp1117.add --logistic --condition rs1117 --noweb
plink --ped dbp.qt.ped --map dbp.map --map3 --out linreg.sex.add --linear --sex --noweb
plink --ped dbp.cc.ped --map dbp.map --map3 --out logreg.sex.inter.add --logistic --sex --interaction --noweb
plink --ped dbp.cc.ped --map dbp.map --map3 --out logreg.snp1112.inter.add --logistic --condition rs1112 --interaction --noweb
R
load("dbp.R")
result.adj = lm (trait ~ sex + rs1112, data=snp.data)
summary(result.adj)
q()
Multifactorial Part 2
plink --ped dbp.cc.ped --map dbp.map --map3 --out logreg.sex.inter.add --logistic --sex --interaction --noweb
plink --ped dbp.cc.ped --map dbp.map --map3 --out logreg.snp1112.inter.add --logistic --condition rs1112 --interaction --noweb
R
result.inter = glm (affection ~ sex * rs1112, family=binomial("logit"), data=snp.data)
summary(result.inter)