replaceJunction {GeneStructureTools} | R Documentation |
Find transcripts containing/overlapping junctions and replace them with alternative junctions
replaceJunction(whippetDataSet, junctionPairs, exons, type = NA)
whippetDataSet |
whippetDataSet generated from |
junctionPairs |
GRanges object with alternative Whippet junctions. Generated by findJunctionPairs() |
exons |
GRanges object made from a GTF containing exon coordinates |
type |
type of Whippet event (AA/AD/AF/AL). Note only one event type should be processed at a time. |
GRanges object with transcripts containing alternative junctions.
Beth Signal
Other whippet splicing isoform creation: addIntronInTranscript
,
findExonContainingTranscripts
,
findIntronContainingTranscripts
,
findJunctionPairs
,
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") transcripts.altAce <- replaceJunction(wds.altAce, jncPairs.altAce, exons, type="AA") wds.altDon <- filterWhippetEvents(wds, eventTypes="AD") jncPairs.altDon <- findJunctionPairs(wds.altDon, type="AD") transcripts.altDon <- replaceJunction(wds.altDon, jncPairs.altDon, exons, type="AD") wds.altFirst <- filterWhippetEvents(wds, eventTypes="AF", psiDelta=0.2) jncPairs.altFirst <- findJunctionPairs(wds.altFirst, type="AF") transcripts.altFirst <- replaceJunction(wds.altFirst, jncPairs.altFirst, exons, type="AF") wds.altLast <- filterWhippetEvents(wds, eventTypes="AL", psiDelta=0.2) jncPairs.altLast <- findJunctionPairs(wds.altLast, type="AL") transcripts.altLast <- replaceJunction(wds.altLast, jncPairs.altLast, exons, type="AL")