Hi,

I'm wondering if there is a way to include potential confounders such as age, sex, genotype, cell composition, etc. into champ.DMR and champ.DMR analysis and if there is, how would I do so?

Thanks!

Hi, as the champ.DMP and champ.DMR can only take one variable as it stands, I would directly modify the source code because it rely on limma : https://rdrr.io/bioc/ChAMP/src/R/champ.DMP.R Particularly, you need to modify the model.matrix <- model.matrix(~ pheno, data=df) by your model with covariates.