addIntronInTranscript {GeneStructureTools} | R Documentation

## Add a retained intron to the transcripts it is skipped by

### Description

Add a retained intron to the transcripts it is skipped by

### Usage

    addIntronInTranscript(flankingExons, exons, whippetDataSet = NULL,
      match = "exact", glueExons = TRUE)

### Arguments

`flankingExons` | data.frame generataed by findIntronContainingTranscripts()
`exons` | GRanges object made from a GTF with ONLY exon annotations (no gene, transcript, CDS etc.)
`whippetDataSet` | whippetDataSet generated from `readWhippetDataSet()`
`match` | what type of match replacement should be done? exact: exact matches to the intron only retain: keep non-exact intron match coordinates in spliced sets, and retain them in retained sets replace: replace non-exact intron match coordinates with event coordinates in spliced sets, and retain in retained sets
`glueExons` | Join together exons that are not seperated by introns?

### Value

GRanges with transcripts containing retained introns

### Author(s)

Beth Signal

### See Also

Other whippet splicing isoform creation: `findExonContainingTranscripts`, `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"]
    g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10

    wds.intronRetention <- filterWhippetEvents(wds, eventTypes="RI")
    exons.intronRetention <- findIntronContainingTranscripts(wds.intronRetention, exons)
    IntronRetentionTranscripts <- addIntronInTranscript(exons.intronRetention, exons,
    whippetDataSet=wds.intronRetention)

    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)

    IntronRetentionTranscripts <-
    addIntronInTranscript(exons.intronRetention, exons, match="retain")

[Package GeneStructureTools version 1.8.0 Index]