I am using dmrseq R package to call for differentially methylated regions (DMR) present in exons from ~8.000 selected genes (starting from Bismark output files).
I have seen the default parameters in dmrseq are adapted to WGBS (data across all the genome).
Since I would be only interested in DMRs across these exons, would you recommend adjusting some dmrseq parameters? Or maybe run dmrseq with the whole genome data and subset to my regions afterwards?
I would prefer to run the analysis only for my regions of interest in order to reduce computational cost, but I am not sure how this could impact my results.
Many thanks in advance!