I'm working with DNA methylation data obtained from the EPIC chip. I've previously used the R package Bumphunter for differentially methylated regions (DMRs). In my current project, I would like to specify a list of specific regions for bumphunter to analyse. In other words, I'm looking for a way to "fix" the regions in advance, and then tell Bumphunter to look at those specific regions - in stead of Bumphunter analysing DMRs genome wide.
Does anyone have any experience or know if it is possible to tweak bumphunter commands to restrict such regions?
I'm very grateful for any response and help to get me a step closer to solve this :)
Thanks for reading!