How to include known covariates?

[xiangzhu]

Many thanks for developing the interesting TreeWAS method and putting together this wonderful set of scripts!

I wonder if I could easily add a few known covariates (e.g. sex, age, genotype-based PCs) in the model given the current implementation. I couldn't find a corresponding file to input the covariate information.

If not, what are the recommended ways of dealing with these covariates when performing TreeWAS analysis?

Thanks in advance for your time and help on this issue!

[ac257]

Hello, Thanks for your interest. We are currently improving the method and implementation on this regard. The way we have performed conditional analysis is described in the supplementary material and this is the approach we followed for the HLA analysis. We found that this worked well for a few covariates but not ideal for fitting many covariates at a time as you request - this is currently not implemented. I will update you as soon as we add this functionality to the public repository.