Do you recommend including principal components as covariates to control for population stratification?

pcarbo / varbvs

Large-scale Bayesian variable selection for R and MATLAB.

http://pcarbo.github.io/varbvs

GNU General Public License v3.0

42 stars 14 forks source link

Do you recommend including principal components as covariates to control for population stratification? #33

Closed garyzhubc closed 3 years ago

garyzhubc commented 3 years ago

Do you recommend including principal components as covariates to control for population stratification? Including PCs does account for the latent population structure but can it also dilute the joint association in the case of multi-SNP analysis?

pcarbo commented 3 years ago

It depends on what type of population structure you are trying to control for, but, yes, in the past we have successfully used PCs as covariates to control for population structure (e.g., in a GWAS with different European populations).