findExonContainingTranscripts {GeneStructureTools} | R Documentation |
Given the location of a whole spliced in exon, find transcripts which can splice out this exon
findExonContainingTranscripts(input, exons, variableWidth = 0, findIntrons = FALSE, transcripts)
input |
whippetDataSet generated from |
exons |
GRanges object made from a GTF containing exon coordinates |
variableWidth |
How many nts overhang is allowed for finding matching exons (default = 0, i.e. complete match) |
findIntrons |
Find transcripts where the event occurs within the intron? |
transcripts |
GRanges object made from a GTF containing transcript coordinates (only required if findIntrons=TRUE) |
data.frame with all overlapping exons
Beth Signal
Other whippet splicing isoform creation: addIntronInTranscript
,
findIntronContainingTranscripts
,
findJunctionPairs
,
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.exonSkip <- filterWhippetEvents(wds, eventTypes="CE",psiDelta = 0.2) exons.exonSkip <- findExonContainingTranscripts(wds.exonSkip, exons, variableWidth=0, findIntrons=FALSE, transcripts) exonFromGRanges <- exons[exons$exon_id == "ENSMUSE00001271768.1"] exons.exonSkip <- findExonContainingTranscripts(exonFromGRanges, exons, variableWidth=0, findIntrons=FALSE, transcripts)