tidyChromosomes {BRGenomics} | R Documentation |
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
|
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 |
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)