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rgcgithub / regenie

regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
https://rgcgithub.github.io/regenie
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covariance of interaction and snp terms #528

Closed Julie-LB closed 4 months ago

Julie-LB commented 4 months ago

I am working on a sex-specific analysis and I would like to perform a meta-analysis of the joint effect of the snp-sex interaction and snp effects (2df test) (the meta-analysis method is Manning et al. 2011). For that meta-analysis, I require the covariance of the snp-sex interaction and snp terms. However, this covariance is not present in the outputs of REGENIE -interaction option.

I was wondering if you have an idea on how to obtain this covariance from REGENIE and if it is possible?

Ojami commented 4 months ago

I am pretty sure REGENIE performs such kDF tests. See here:

𝐻0:𝛽=𝛾=0 which tests both main and interaction effects for the SNP

Julie-LB commented 4 months ago

Yes, it does, but it only provides the chi square test and P-value, but not he covariance of the main and interaction terms.

Ojami commented 4 months ago

In that case you can use --print-vcov flag (undocumented) which write variance-covariance matrix to a file. Note that you may apply --no-condtl depending on the interaction term you're applying.