How does calculateDiffMeth cope with multiple treatment groups (>2) ?

[erikras12]

Hello,

I ran calculateDiffMeth with a treatment vector length of 8 and I am unsure how the comparisons are made in this context. Are all comparisons made or are 7 of the treatments compared to just one etc. ?

[alexg9010]

Hi @erikras12,

You are basically running a logistic regression with eight groups. The methylation difference at each given site will correspond to the maximal methylation difference between the groups: https://github.com/al2na/methylKit/blob/9620cd686a14483f2158c75805c952d066c7b7f8/R/diffMeth.R#L306-L312

We did not implement a function to run all comparisons, but you may achieve this manually by reorganizing your objects in a loop.

Best Alex