findIntronContainingTranscripts: Given the location of a whole retained intron, find...

In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description

Given the location of a whole retained intron, find transcripts which splice out this intron

Usage

findIntronContainingTranscripts(input, exons, match = "exact")

Arguments

input	whippetDataSet generated from readWhippetDataSet() or a Granges of intron coordinates
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

Value

data.frame with all flanking exon pairs

Author(s)

Beth Signal

See Also

Other whippet splicing isoform creation: addIntronInTranscript, findExonContainingTranscripts, findJunctionPairs, replaceJunction, skipExonInTranscript

Examples

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)

GeneStructureTools documentation built on Nov. 8, 2020, 6:04 p.m.