filterChromosomes

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

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

Arguments

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

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(regioneR)
Loading required package: memoise
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/regioneR/filterChromosomes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: filterChromosomes
> ### Title: filterChromosomes
> ### Aliases: filterChromosomes
> 
> ### ** Examples
> 
> 
> g <- getGenomeAndMask("hg19")$genome
> listChrTypes()
Homo sapiens (hg): autosomal, canonical 
Mus musculus (mm): autosomal, canonical 
Bos taurus (bosTau): autosomal, canonical 
Caenorhabditis elegans (ce): autosomal, canonical 
Danio rerio (danRer): canonical 
Macaca mulata (rheMac): autosomal, canonical 
Rattus norvegicus (rn): autosomal, canonical 
Saccharomyces cerevisiae (sacCer): autosomal, canonical 
Drosophila melanogaster (dm): autosomal, canonical 
Pan troglodytes (panTro): autosomal, canonical 
> g <- filterChromosomes(g, chr.type="autosomal", organism="hg19")
> g <- filterChromosomes(g, keep.chr=c("chr1", "chr2", "chr3"))
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>