I see that it was discussed here: A: Dmr (Differentially Methylated Regions) Identification Software but I would like to dig a little deeper into that, because I couldn't find a satisfying answer yet.
So - what statistical test would you choose for DMR (differentially methylated regions) annotation? Meaning you have a 2X2 table with column labels `WT` and `mutant`, and row labels `methylated` and `not methylated`, each cell has a count for a single region. You need to test whether methylation is dependent on the mutation.
I see that `methylkit` uses Fisher's Exact Test, but that test doesn't make sense to me. Why would DMR's behave hyper-geometrically? This assumes that the background set from which you sample is finite, right? And that's not the case with methylation - you can (theoretically) sample as much as you want, like coin flipping.
Am I right? What test would you use?
Thanks a lot, Amit