Can exactTest be safely replaced with glmQLFit to add batch effect correction? #110
Description
Hi,
I'm using DiffAnalysisHiChIP.r and wanted to ask if the exactTest() function in ApplyEdgeR() can be safely replaced with glmQLFit()/glmQLFTest() in order to include batch as a covariate in the design matrix (e.g., design <- model.matrix(~Batch + GroupDistrVec)). Would this break any assumptions in downstream steps?
Thank you!