Question: Gene environment interaction model with genetic relation matrix (GRM) as a random covariate
0
gravatar for alioniya
18 months ago by
alioniya0
alioniya0 wrote:

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!

gcta snp interacion gwas • 407 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by alioniya0
1

I think GEMMA enables both

ADD REPLYlink written 18 months ago by Asaf8.5k

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

ADD REPLYlink written 15 months ago by alioniya0

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

ADD REPLYlink written 15 months ago by Asaf8.5k
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