I would like to perform HAllA on a two datasets (both of which quantitative variables). However, I also have qualitative covariates that I would like to adjust for prior to HAllA. I read the manuscript for Lloyd-Price et al. 2019 and some other manuscripts out there, and it says that the dataset needs to first be “residualized” based on a linear mixed effects model from the differential abundance analysis, and the HAllA tutorial mentions that any covariates need to be regressed out using lmer command from the lme4 package.
My question is how do we take the information from the lmer output (e.g. residuals) and change the -X and -Y inputs for HAllA? I am not entirely sure what pieces of information from the lmer output we take to apply it to the halla inputs. Specifically, the Lloyd-Price manuscript mentioned " Pearson’s residual values from the above linear mixed effects models were retained for use in [HAllA]," but how does this value get incorporated into my quantitative measurements for my -X and -Y datasets?
I am relatively new to HAllA analysis so I would appreciate any help about this. Thanks so much!