inst/scripts/create_species_seqlengths_granges.R

In biobenkj/compartmap: Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

##Create the GRanges objects for each supported species
#The goal is to create a lightweight GRanges object for seqlengths
#rather than having to keep larger packages (e.g. BSgenome) as
#dependencies. It also speeds up the build system.

#hg19
library(Homo.sapiens)

hg19.gr <- as(seqinfo(Homo.sapiens), "GRanges")

#hg38
library(BSgenome.Hsapiens.UCSC.hg38)

hg38.gr <- as(seqinfo(BSgenome.Hsapiens.UCSC.hg38),
              "GRanges")

#mm9
library(BSgenome.Mmusculus.UCSC.mm9)

mm9.gr <- as(seqinfo(BSgenome.Mmusculus.UCSC.mm9),
             "GRanges")

#mm10
library(Mus.musculus)

mm10.gr <- as(seqinfo(Mus.musculus), "GRanges")

#save
save(hg19.gr, file = "~/git_repos/compartmap/data/hg19_gr.rda")
save(hg38.gr, file = "~/git_repos/compartmap/data/hg38_gr.rda")
save(mm9.gr, file = "~/git_repos/compartmap/data/mm9_gr.rda")
save(mm10.gr, file = "~/git_repos/compartmap/data/mm10_gr.rda")