replaceJunction {GeneStructureTools} | R Documentation

## Find transcripts containing/overlapping junctions and replace them with alternative junctions

### Description

Find transcripts containing/overlapping junctions and replace them with alternative junctions

### Usage

    replaceJunction(whippetDataSet, junctionPairs, exons, type = NA)

### Arguments

`whippetDataSet` | whippetDataSet generated from `readWhippetDataSet()`
`junctionPairs` | GRanges object with alternative Whippet junctions. Generated by findJunctionPairs()
`exons` | GRanges object made from a GTF containing exon coordinates
`type` | type of Whippet event (AA/AD/AF/AL). Note only one event type should be processed at a time.

### Value

GRanges object with transcripts containing alternative junctions.

### Author(s)

Beth Signal

### See Also

Other whippet splicing isoform creation: `addIntronInTranscript`, `findExonContainingTranscripts`, `findIntronContainingTranscripts`, `findJunctionPairs`, `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.altAce <- filterWhippetEvents(wds, eventTypes="AA")
    jncPairs.altAce <- findJunctionPairs(wds.altAce, type="AA")
    transcripts.altAce <- replaceJunction(wds.altAce, jncPairs.altAce, exons, type="AA")

    wds.altDon <- filterWhippetEvents(wds, eventTypes="AD")
    jncPairs.altDon <- findJunctionPairs(wds.altDon, type="AD")
    transcripts.altDon <- replaceJunction(wds.altDon, jncPairs.altDon, exons, type="AD")

    wds.altFirst <- filterWhippetEvents(wds, eventTypes="AF", psiDelta=0.2)
    jncPairs.altFirst <- findJunctionPairs(wds.altFirst, type="AF")
    transcripts.altFirst <- replaceJunction(wds.altFirst, jncPairs.altFirst, exons, type="AF")

    wds.altLast <- filterWhippetEvents(wds, eventTypes="AL", psiDelta=0.2)
    jncPairs.altLast <- findJunctionPairs(wds.altLast, type="AL")
    transcripts.altLast <- replaceJunction(wds.altLast, jncPairs.altLast, exons, type="AL")

[Package GeneStructureTools version 1.6.0 Index]