transcripts: Extracts transcript information (exon start and ends) from an...

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.

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

See Also

genePlot to plot the resulting transcripts

Examples

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

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