How to calculate covariance between betas for GxE interaction using PLINK 2.0

Question

[Apprentice]

Hi.

I would like to perform genome-wide meta-analysis of GxE interaction across 5 cohorts.

I'm going to use a joint meta-analysis of Mannig et al. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312394/) I know that the method needs SNP beta and SNP×E beta and covariance between the betas.

I could obtained SNP beta and the SNP×E beta from each cohort using PLINK 2.0, but I don't know how to calculate covariance using PLINK 2.0.

Could you tell me how to compute the covariance?

Answer 1

[chrchang523]

This is not currently implemented in PLINK, sorry.

[Apprentice]

Thank you for your quick response. I got it.