Help needed for Interaction analysis (linear regression)

Question

[Mahan]

Apologize me if its a silly query

Hi friends

I'm trying to generate a risk score (weighted by the beta of each SNP) using a set of 28 SNPs and my model looks like this

--adjust --bfile project --covar pheno_file --covar-name Gender, Age,PC1,PC2,PC3 --linear --out file --pheno pheno_file --pheno-name Height

I would like to include an interaction term for SNP*Gender in my model.

With this background, I would like to know

1. The appropriate syntax for the interaction analysis

2. Which beta value I should use to compute the weighted risk score further?

Thanks in advance M

[Kevin Blighe]

If you are using Plink version 1.9 or greater, then the syntax is:

plink --bfile mydata --linear interaction --covar tmp.cov

This is in the manual: https://www.cog-genomics.org/plink2/assoc

With regard to which beta coefficients to choose, that depends n which interactions are statistically significant. It also depends on what your study is about, i.e., the hypothesis that you're testing. So, what is your hypothesis an what is the gal of your study?