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]