addIntronInTranscript {GeneStructureTools} | R Documentation |
Add a retained intron to the transcripts it is skipped by
addIntronInTranscript(flankingExons, exons, whippetDataSet = NULL, match = "exact", glueExons = TRUE)
flankingExons |
data.frame generataed by findIntronContainingTranscripts() |
exons |
GRanges object made from a GTF with ONLY exon annotations (no gene, transcript, CDS etc.) |
whippetDataSet |
whippetDataSet generated from |
match |
what type of match replacement should be done? exact: exact matches to the intron only retain: keep non-exact intron match coordinates in spliced sets, and retain them in retained sets replace: replace non-exact intron match coordinates with event coordinates in spliced sets, and retain in retained sets |
glueExons |
Join together exons that are not seperated by introns? |
GRanges with transcripts containing retained introns
Beth Signal
Other whippet splicing isoform creation: findExonContainingTranscripts
,
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$type=="exon"] g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 wds.intronRetention <- filterWhippetEvents(wds, eventTypes="RI") exons.intronRetention <- findIntronContainingTranscripts(wds.intronRetention, exons) IntronRetentionTranscripts <- addIntronInTranscript(exons.intronRetention, exons, whippetDataSet=wds.intronRetention) exonsFromGRanges <- exons[exons$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) IntronRetentionTranscripts <- addIntronInTranscript(exons.intronRetention, exons, match="retain")