getIsland: getIsland returns the island id associated to a given entrez...

In casper: Characterization of Alternative Splicing based on Paired-End Reads

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

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)

casper documentation built on Dec. 17, 2020, 2:01 a.m.