PLINK linear association

Question

[ebrudermanver]

When I run PLINK command

plink --noweb --file mysnps --linear --standard-beta --pheno randgeneexpr.txt --out mysnps

does PLINK perform an association test for each SNP in the mysnps file separately (univariate linear regression), or all SNPs in the mysnps file used as input in a multivariate linear regression (aka multiple regression)?

Thanks.

Answer 1

[chrchang523]

PLINK performs univariate linear regression. (When covariates are added with --covar, they are present in all of the linear regressions.)

[ebrudermanver]

I see, thanks. How can I use all SNPs in the mysnps file in a multiple regression to predict phenotype? I have no other covariates to include.