findExonContainingTranscripts {GeneStructureTools} | R Documentation

## Given the location of a whole spliced in exon, find transcripts which can splice out this exon

### Description

Given the location of a whole spliced in exon, find transcripts which can splice out this exon

### Usage

    findExonContainingTranscripts(input, exons, variableWidth = 0,
      findIntrons = FALSE, transcripts)

### Arguments

`input` | whippetDataSet generated from `readWhippetDataSet()` or a Granges of exon coordinates
`exons` | GRanges object made from a GTF containing exon coordinates
`variableWidth` | How many nts overhang is allowed for finding matching exons (default = 0, i.e. complete match)
`findIntrons` | Find transcripts where the event occurs within the intron?
`transcripts` | GRanges object made from a GTF containing transcript coordinates (only required if findIntrons=TRUE)

### Value

data.frame with all overlapping exons

### Author(s)

Beth Signal

### See Also

Other whippet splicing isoform creation: `addIntronInTranscript`, `findIntronContainingTranscripts`, `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$type=="exon"]
    transcripts <- gtf[gtf$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)

    exonFromGRanges <- exons[exons$exon_id == "ENSMUSE00001271768.1"]
    exons.exonSkip <- findExonContainingTranscripts(exonFromGRanges, exons,
    variableWidth=0, findIntrons=FALSE, transcripts)

[Package GeneStructureTools version 1.14.0 Index]