I'm a big fan of
bsseq because it is exactly the data structure I need for a package I maintain (
methylSig) that tests for differential methylation (at CpGs and over regions).
As of the Bioc 3.7 release it appears that a check in the
BSseq constructor was added (I don't see a reference to it in the
if(any(width(gr) != 1)) stop("'gr' needs to have widths of 1")
It was incredibly convenient to be able to create
BSseq objects that aggregated CpGs over regions so that there was still a unified methylation object to access and manipulate.
I would like to request that this check be removed to enable
BSseq objects with ranges greater than 1bp. Of course, I understand there may be intra-package consistency reasons for the change, but I figured it was worth a shot to ask because I think there is value in
BSseq objects that represent methylation over regions.
A quick note, I also posted a GitHub issue because I wasn't sure which got checked faster (https://github.com/hansenlab/bsseq/issues/68)