filterChromosomes

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Description

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")

Usage

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

Arguments

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.

Value

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.

See Also

getGenomeAndMask, listChrTypes getChromosomesByOrganism

Examples

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

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