findIntronContainingTranscripts {GeneStructureTools} | R Documentation |
Given the location of a whole retained intron, find transcripts which splice out this intron
findIntronContainingTranscripts(input, exons, match = "exact")
input |
whippetDataSet generated from |
exons |
GRanges object made from a GTF with ONLY exon annotations (no gene, transcript, CDS etc.) |
match |
what type of matching to perform? exact = only exons which bound the intron exactly, introns = any exon pairs which overlap the intron, all = any exon pairs AND single exons which overlap the intron |
data.frame with all flanking exon pairs
Beth Signal
Other whippet splicing isoform creation: addIntronInTranscript
,
findExonContainingTranscripts
,
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$type=="exon"] g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 wds.intronRetention <- filterWhippetEvents(wds, eventTypes="RI") exons.intronRetention <- findIntronContainingTranscripts(input=wds.intronRetention, exons) exonsFromGRanges <- exons[exons$transcript_id=="ENSMUST00000139129.8" & exons$exon_number %in% c(3,4)] intronFromGRanges <- exonsFromGRanges[1] GenomicRanges::start(intronFromGRanges) <- GenomicRanges::end(exonsFromGRanges[exonsFromGRanges$exon_number==3]) GenomicRanges::end(intronFromGRanges) <- GenomicRanges::start(exonsFromGRanges[exonsFromGRanges$exon_number==4]) exons.intronRetention <- findIntronContainingTranscripts(intronFromGRanges, exons)