transcripts: Extracts transcript information (exon start and ends) from an `annotatedGenome` object, either for all transcripts or only those corresponding to a given island or transcript.

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.

transcripts retrieves all stored transcripts for a given transcript or island.

matchTranscripts finds transcripts in queryDB matching a transcript in subjectDB. The best match for each transcript in subjectDB is returned, unless difference in bp is >maxbp

Usage

transcripts(genomeDB, txid, islandid)
matchTranscripts(queryDB, subjectDB, maxbp=10)

Arguments

genomeDB

Object of class annotatedGenome

txid

Character indicating transcript identifier (optional)

islandid

Character indicating island identifier (optional)

queryDB

annotatedGenome with query transcripts

subjectDB

annotatedGenome with potentially matching transcripts

maxbp

Maximum difference in bp for transcripts to be matched

Value

IRangesList where each element in the list corresponds to a different transcript.

Methods

signature(genomeDB = "annotatedGenome", txid="missing", islandid="missing"): Return exons for all transcripts in genomeDB
signature(genomeDB = "annotatedGenome", txid="character", islandid="missing"): Return exons for transcript txid
signature(genomeDB = "annotatedGenome", txid="missing", islandid="character"): Return exons for all transcripts in island islandid

Examples

Run this code

data(hg19DB)
txs <- transcripts(txid="NM_005158",genomeDB=hg19DB)
txs