I have 2 questions relative to the DSS package, which I am currently using in order to analyse methylation data from RRBS:
1) In the 3.3 section of the DSS vignette, it is mentioned that smoothing is not recommended for RRBS data (in the DMLTest() function). However, in the FAQ at the end of the vignette, it is said that smoothing is always recommended, even for RRBS. Thus I am a little bit confused: should I put FALSE or TRUE for the smoothing option?
2) Is it possible to collapse CpG sites, like do the option strandCollapse = TRUE in the bsseq::read.bismark() function?
Any help would be very welcome.