getIsland returns the island id associated to a given entrez or transcript id in an annotatedGenome object. getChr indicates the chromosome for a given Entrez, transcript or island id.

Description

annotatedGenome objects store information regarding genes and transcripts. When there's an overlap in exons between several genes, these genes are grouped into gene islands. getIsland retrieves the island to which each gene or transcript was assigned, while getChr indicates the chromosome.

Usage

getIsland(entrezid, txid, genomeDB)
getChr(entrezid, txid, islandid, genomeDB)

Arguments

Value

Character with island identifier

Methods

signature(entrezid='character',txid='missing',genomeDB='annotatedGenome')

Return island id for given Entrez identifier

signature(entrezid='missing',txid='character',genomeDB='annotatedGenome')

Return island id for given transcript identifier (RefSeq)

signature(entrezid='character',txid='missing',islandid='missing',genomeDB='annotatedGenome')

Return chromosome for given Entrez identifier (RefSeq)

signature(entrezid='missing',txid='character',islandid='missing',genomeDB='annotatedGenome')

Return chromosome for given transcript identifier (RefSeq)

signature(entrezid='missing',txid='missing',islandid='character',genomeDB='annotatedGenome')

Return chromosome for given island identifier

signature(entrezid='character',txid='missing',islandid='missing')

Return chromosome for given Entrez identifier

signature(entrezid='missing',txid='character',islandid='missing')

Return chromosome for given transcript identifier (RefSeq)

signature(entrezid='missing',txid='character',islandid='missing')

Return chromosome for given island identifier

Examples

data(hg19DB)
getIsland(entrezid="27",genomeDB=hg19DB)
getIsland(txid="NM_005158",genomeDB=hg19DB)

getChr(entrezid="27",genomeDB=hg19DB)
getChr(txid="NM_005158",genomeDB=hg19DB)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(casper)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
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: GenomicRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/casper/getIsland.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getIsland
> ### Title: getIsland returns the island id associated to a given entrez or
> ###   transcript id in an annotatedGenome object. getChr indicates the
> ###   chromosome for a given Entrez, transcript or island id.
> ### Aliases: getIsland getIsland,character,missing,annotatedGenome-method
> ###   getIsland,missing,character,annotatedGenome-method getChr
> ###   getChr-method getChr,character,missing,missing,annotatedGenome-method
> ###   getChr,missing,character,missing,annotatedGenome-method
> ###   getChr,missing,missing,missing,annotatedGenome-method
> ###   getChr,missing,missing,character,annotatedGenome-method
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(hg19DB)
> getIsland(entrezid="27",genomeDB=hg19DB)
[1] "463"
> getIsland(txid="NM_005158",genomeDB=hg19DB)
[1] "463"
> 
> getChr(entrezid="27",genomeDB=hg19DB)
[1] "chr1"
> getChr(txid="NM_005158",genomeDB=hg19DB)
[1] "chr1"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>