findJunctionPairs {GeneStructureTools} | R Documentation |
Find junctions that pair with each end of an AA (alt. acceptor) or AD (alt. donor) whippet range Find junctions that pair with the upsteam/downstream exon of an AF (alt. first exon) or an AL (alt. last exon)
findJunctionPairs(whippetDataSet, jncCoords, type = NA)
whippetDataSet |
whippetDataSet generated from |
jncCoords |
GRanges object with Whippet junctions. Generated by readWhippetJNCfiles() |
type |
type of Whippet event (AA/AD/AF/AL). Note only one event type should be processed at a time. |
GRanges object with alternative junctions. Each event should have a set of X (for which the psi measurement is reported) junctions, and alternative Y junctions.
Beth Signal
Other whippet splicing isoform creation: addIntronInTranscript
,
findExonContainingTranscripts
,
findIntronContainingTranscripts
,
replaceJunction
,
skipExonInTranscript
whippetFiles <- system.file("extdata","whippet/", package = "GeneStructureTools") wds <- readWhippetDataSet(whippetFiles) wds <- filterWhippetEvents(wds) gtf <- rtracklayer::import(system.file("extdata","example_gtf.gtf", package = "GeneStructureTools")) exons <- gtf[gtf$type=="exon"] transcripts <- gtf[gtf$type=="transcript"] g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 wds.altAce <- filterWhippetEvents(wds, eventTypes="AA") jncPairs.altAce <- findJunctionPairs(wds.altAce, type="AA") wds.altDon <- filterWhippetEvents(wds, eventTypes="AD") jncPairs.altDon <- findJunctionPairs(wds.altDon, type="AD") wds.altFirst <- filterWhippetEvents(wds, eventTypes="AF", psiDelta=0.2) jncPairs.altFirst <- findJunctionPairs(wds.altFirst, type="AF") wds.altLast <- filterWhippetEvents(wds, eventTypes="AL", psiDelta=0.2) jncPairs.altLast <- findJunctionPairs(wds.altLast, type="AL")