I would like to use the "promoters" function in the "GenomicRanges" package to generate "GRanges" objects, but I would like these objects to have "REFSEQ" names rather than UCSC-style names.
This gives me UCSC-style names:
a1 <- promoters(Mus.musculus)
Trying the following sort of approach, based on looking at the columns in Mus.musculus, allows me to change some of the metadata columns, but I quickly end up with error messages saying that the columns I'm trying to add are unavailable:
a2 <- promoters(Mus.musculus, columns = c("TXID", "TXSTART", "GENEID"))
Thanks so very much, Robert! That really helps.