How do define genome

[qliugithub]

Nice packages!
From the help message, I find the genome arguments only mm9 and hg38, How Can I define the other genomes, thanks.

[cnluzon]

Thanks for the feedback! The only functions thatuse the genome as parameter are the bins functions (bw_bins, plot_bw_bins_*), since they need to know the chromosomes and lengths, but this information is pulled via Seqinfo from the GenomeInfoDb package so in reality, anything supported by the package works. I had not documented this before because we use it for mainly those genomes, so I did not have bigWigs from other genomes, but it should work for other genomes too, like "dm3" or "GRCh38". At least, I checked that build_bins function works, so let me know if bw_bins does not work for your files. See the Seqinfo documentation for more examples: https://www.rdocumentation.org/packages/GenomeInfoDb/versions/1.8.3/topics/seqinfo

[cnluzon]

Since this works, I will close this issue.

Note that sometimes GenomeInfoDb updates make build_bins crash but this eventually gets fixed. In the case where it does not, one could use bw_loci* functions with a custom build GRanges object. If one has a typical chromsizes file, this can be done this way using SeqInfo and GenomicRanges::tileGenome function.

gsizes <- read.table("mm39.chrom.sizes")
# This builds a Seqinfo object (needs GenomeInfoDb)
sq <- Seqinfo(seqnames = gsizes$V1, seqlengths = gsizes$V2)
gr_tiles <- GenomicRanges::tileGenome(sq, tilewidth = 10000, cut.last.tile.in.chrom = TRUE)