skipExonInTranscript {GeneStructureTools}R Documentation

Remove and include a skipped exon from the transcripts it overlaps

Description

Remove and include a skipped exon from the transcripts it overlaps

Usage

skipExonInTranscript(skippedExons, exons, glueExons = TRUE,
  whippetDataSet = NULL, match = "exact")

Arguments

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 readWhippetDataSet()

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

Value

GRanges with transcripts skipping exons

Author(s)

Beth Signal

See Also

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

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$type=="exon"]
transcripts <- gtf[gtf$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")

[Package GeneStructureTools version 1.8.0 Index]