13 months ago by
If this is human, perhaps you can consider the UCSC CpG Islands (and you can get some gene mappings through Bioconductor)?
The RRBS coverage may also tend to be in certain blocks, so you could also use distance to the gene. However, I think that knowing about the CpG Islands (or more specific boundaries for regions of higher coverage) may be helpful?
Either way, I am assuming you are asking about how to create the genome ranges object ("refGR" in the example for
regionCounts(meth, regions=refGR), where "meth" is the result of running
myobj = methRead() and
You can use anything with the relevant information, but I think this will work for a bed file (with names assuming that you had your own set of "promoter" regions - although an "island" table would work just as well):
refGR = GRanges(Rle(promoter.table$V1),
For just the CpG island part, I think you want to download "CpG Islands" under "Regulation" from the Table Browser: