I have used bump hunter function for two populations (control and disease represented by status column) using the following formula
designMatrix <- model.matrix(~ status)
For each of control and disease populations,within each population, I have subpouations treated with different drugs
I would like to identify DMRs between control and disease considering these conditions (drugs)
I made the design matrix as follows:
designMatrix <- model.matrix(~ status+condition)
I found that the out put is very similar. I would like to know is it possible to identify DMRs between disease and normal considering different treatments using bump hunter?