covariate dataset

[rthapa1]

Hi,

Thank you for the wonderful package. Is there any way to add population structure and kinship matrix as covariate?

Thanks

[Hua Zhou]

You can certainly add principal components as covariates. By kinship matrix, do you mean using it as a variance component? Current package cannot handle random effects or variance component.

[rthapa1]

Yes, I want to add the kinship matrix as the random effect.

[rthapa1]

Is there a way to add a population structure matrix instead of PCA as a fixed effect?

[Hua Zhou]

By population structure matrix, do you mean the empirical kinship matrix such as the genetic relation matrix (GRM) GG'/S where G is the column centered and scaled genotype matrix and S is number of SNPs? I don't see a way incorporate this matrix as fixed effects.

[rthapa1]

Thank you Zhou, it looks like MASS package doesn't allow to add random effects.