casper (version 2.6.0)

getIsland: 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

entrezid

Character indicating single Entrez identifier. Can be left missing and specify another identifier instead.

txid

Character indicating a single RefSeq transcript identifier. Can be left missing and specify another identifier instead.

islandid

Character indicating the gene island indentifier. Can be left missing and specify another identifier instead.

genomeDB

Object of class annotatedGenome

Value

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)