skipExonInTranscript {GeneStructureTools} | R Documentation |
Remove and include a skipped exon from the transcripts it overlaps
skipExonInTranscript(skippedExons, exons, glueExons = TRUE, whippetDataSet = NULL, match = "exact")
skippedExons |
data.frame generataed by findExonContainingTranscripts() |
exons |
GRanges object made from a GTF with ONLY exon annotations (no gene, transcript, CDS etc.) |
glueExons |
Join together exons that are not seperated by exons? |
whippetDataSet |
whippetDataSet generated from |
match |
what type of match replacement should be done? exact: exact matches to the skipped event only, also removes any intron overlaps skip: keep non-exact exon match coordinates in included sets, and skip them in skipped sets replace: replace non-exact exon match coordinates with event coordinates in included sets, and skip them in skipped sets |
GRanges with transcripts skipping exons
Beth Signal
Other whippet splicing isoform creation: addIntronInTranscript
,
findExonContainingTranscripts
,
findIntronContainingTranscripts
,
findJunctionPairs
,
replaceJunction
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.exonSkip <- filterWhippetEvents(wds, eventTypes="CE",psiDelta = 0.2) exons.exonSkip <- findExonContainingTranscripts(wds.exonSkip, exons, variableWidth=0, findIntrons=FALSE, transcripts) ExonSkippingTranscripts <- skipExonInTranscript(exons.exonSkip, exons, whippetDataSet=wds.exonSkip) exonFromGRanges <- exons[exons$exon_id == "ENSMUSE00001271768.1"] exons.exonSkip <- findExonContainingTranscripts(exonFromGRanges, exons, variableWidth=0, findIntrons=FALSE, transcripts) ExonSkippingTranscripts <- skipExonInTranscript(exons.exonSkip, exons, match="skip")