getChromosomesByOrganism

Description

Function to obtain a list of organisms with their canonical and (when applicable) the autosomal chromosome names. This function is not usually used by the end user directly but through the filterChromosomes function.

Usage

getChromosomesByOrganism()

Value

a list with the organism as keys and the list of available chromosome sets as values

See Also

getGenome, filterChromosomes

Examples

chrsByOrg <- getChromosomesByOrganism() 
chrsByOrg[["hg"]]
chrsByOrg[["hg"]][["autosomal"]]

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/getChromosomesByOrganism.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getChromosomesByOrganism
> ### Title: getChromosomesByOrganism
> ### Aliases: getChromosomesByOrganism
> 
> ### ** Examples
> 
> 
> chrsByOrg <- getChromosomesByOrganism() 
> chrsByOrg[["hg"]]
$autosomal
 [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9" 
[10] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18"
[19] "chr19" "chr20" "chr21" "chr22"

$canonical
 [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9" 
[10] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18"
[19] "chr19" "chr20" "chr21" "chr22" "chrX"  "chrY" 

$org.name
[1] "Homo sapiens"

> chrsByOrg[["hg"]][["autosomal"]]
 [1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9" 
[10] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18"
[19] "chr19" "chr20" "chr21" "chr22"
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>