filterChromosomes: filterChromosomes
In regioneR: Association analysis of genomic regions based on permutation tests

Description Usage Arguments Value See Also Examples

Filters the chromosomes in a region set. It can either filter using a predefined chromosome set (e.g. "autosomal chromosomes in Homo sapiens") or using a custom chromosome set (e.g. only chromosomes "chr22" and "chrX")

1	filterChromosomes(A, organism="hg", chr.type="canonical", keep.chr=NULL)

`A`	a region set in any of the formats accepted by `toGRanges` (`GenomicRanges`, `data.frame`, etc...)
`organism`	a character indicating the organism from which to get the predefined chromosome sets. It can be the organism code as used in `BSgenome` (e.g. hg for human, mm for mouse...) or the full genome assembly identifier, since any digit will be removed to get the organism code.
`chr.type`	a character indicating the specific chromosome set to be used. Usually "autosomal" or "canonical", althought other values could be available for certain organisms.
`keep.chr`	is a character vector stating the names of the chromosomes to keep. Any chromosome not in the vector will be filtered out. If keep.chr is supplied, organism and chr.type are ignored.

A GRanges object containing only the regions in the original region set belonging to the selected chromosomes. All regions in non selected chromosomes are removed.

getGenomeAndMask, listChrTypes getChromosomesByOrganism

g <- getGenomeAndMask("hg19")$genome
listChrTypes()
g <- filterChromosomes(g, chr.type="autosomal", organism="hg19")
g <- filterChromosomes(g, keep.chr=c("chr1", "chr2", "chr3"))