Gene environment interaction model with genetic relation matrix (GRM) as a random covariate

Question

[alioniya]

I'm performing GWAS analysis with binary phenotype. In my cohort there are related individuals, which we don't want to exclude. To adjust for population substructure, we use mixed linear model in GCTA software, using genetic relation matrix (GRM) as a random covariate.

Also we need to use the logistic regression model for gene*environment interaction. Could you tell please, which software can I use to solve both problems:

1. use genetic relation matrix (GRM) as a random covariate in the linear mixed model
2. use the logistic regression model for gene*environment interaction

I tried plink, GCTA, SNPtest - it doesn't allow to include both parameters.

Thank you!

[Asaf]

I think GEMMA enables both

[alioniya]

Could you also tell plsm, LMM model in GEMMA works for binary outcome?

[Asaf]

I don't see a reason why it shouldn't work, you'll have to take a look at the manual for specifics