transcripts {casper} | R Documentation |
annotatedGenome
object,
either for all transcripts or only those corresponding
to a given island or transcript.
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
transcripts(genomeDB, txid, islandid) matchTranscripts(queryDB, subjectDB, maxbp=10)
genomeDB |
Object of class |
txid |
Character indicating transcript identifier (optional) |
islandid |
Character indicating island identifier (optional) |
queryDB |
|
subjectDB |
|
maxbp |
Maximum difference in bp for transcripts to be matched |
IRangesList
where each element in the list corresponds to a
different transcript.
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
genePlot
to plot the resulting transcripts
data(hg19DB) txs <- transcripts(txid="NM_005158",genomeDB=hg19DB) txs