findIntronContainingTranscripts {GeneStructureTools} | R Documentation

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

### 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)

[Package GeneStructureTools version 1.6.0 Index]