tidyChromosomes: Remove odd chromosomes from GRanges objects
In BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data

Description Usage Arguments Details Value Author(s) See Also Examples

This convenience function removes non-standard, mitochondrial, and/or sex chromosomes from any GRanges object.

tidyChromosomes(
  gr,
  keep.X = TRUE,
  keep.Y = TRUE,
  keep.M = FALSE,
  keep.nonstandard = FALSE,
  genome = NULL
)

`gr`	Any GRanges object, or any another object with associated `seqinfo` (or a `Seqinfo` object itself). The object should typically have a standard genome associated with it, e.g. `genome(gr) <- "hg38"`. `gr` can also be a list of such GRanges objects.
`keep.X, keep.Y, keep.M, keep.nonstandard`	Logicals indicating which non-autosomes should be kept. By default, sex chromosomes are kept, but mitochondrial and non-standard chromosomes are removed.
`genome`	An optional string that, if supplied, will be used to set the genome of `gr`.

Standard chromosomes are defined using the standardChromosomes function from the GenomeInfoDb package.

A GRanges object in which both ranges and seqinfo associated with trimmed chromosomes have been removed.

Mike DeBerardine

GenomeInfoDb::standardChromosomes

# make a GRanges
chrom <- c("chr2", "chr3", "chrX", "chrY", "chrM", "junk")
gr <- GRanges(seqnames = chrom,
              ranges = IRanges(start = 2*(1:6), end = 3*(1:6)),
              strand = "+",
              seqinfo = Seqinfo(chrom))
genome(gr) <- "hg38"

gr

tidyChromosomes(gr)

tidyChromosomes(gr, keep.M = TRUE)

tidyChromosomes(gr, keep.M = TRUE, keep.Y = FALSE)

tidyChromosomes(gr, keep.nonstandard = TRUE)