plink analysis including covariates and gxe

Question

[ddzhangzz]

I would conduct a GWAS using plink with covariates and gxe terms. Here is part of phenotypic data:

   FID  IID luperml2wk18 luperml2chg rotaarm sex
1 1001 1001        7.008      6.4601       1   2
2 1002 1002        1.823      1.6745       1   1
3 1003 1003        2.706      1.2638       1   2
4 1004 1004        3.316      3.5770       0   1
5 1005 1005        1.095     -0.2104       0   1
6 1007 1007        1.369      1.1616       0   2
...

I would like a model such that:

luperml2wk18=SNPi+sex+rotaarm+SNPi*rotaarm

where sex is a covariate and rotaarm is dummy variable of treatment/placebo and SNPi*rotaarm is a gxe term. I am confused whether I should take rotaarm as a covariate using --covar or a stratification using --within. I have tried this:

plink --noweb --bfile $GENO --allow-no-sex --pheno $PHENO --pheno-name luperml2wk18 \
      --covar $PHENO --covar-name sex\
      --bd --within rotaarm.txt\
      --gxe --covar rotaarm.txt \
      --linear --out IgA_logwk18_Malchip_gxe

But I got error message say:

** Unused command line option: --covar 
** Unused command line option: rotaarm.txt

Why can't I include the --covar here?

Answer 1

[chrchang523]

--covar appears twice in your command line.