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")

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