replaceJunction: Find transcripts containing/overlapping junctions and replace...

In betsig/GeneStructureTools: Tools for spliced gene structure manipulation and analysis

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(), alterTranscriptStartEnds(), findExonContainingTranscripts(), findIntronContainingTranscripts(), findJunctionPairs(), skipExonInTranscript()

Examples

gtf <- rtracklayer::import(system.file("extdata", "gencode.vM25.small.gtf", package = "GeneStructureTools"))
exons <- gtf[gtf$type == "exon"]
g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10

whippetFiles <- system.file("extdata", "whippet_small/",
    package = "GeneStructureTools"
)
wds <- readWhippetDataSet(whippetFiles)

wds.altAce <- filterWhippetEvents(wds, eventTypes = "AA", psiDelta = 0.1, probability = 0.8)
jncPairs.altAce <- findJunctionPairs(wds.altAce, type = "AA")
transcripts.altAce <- replaceJunction(wds.altAce, jncPairs.altAce, exons, type = "AA")

wds.altDon <- filterWhippetEvents(wds, eventTypes = "AD", psiDelta = 0.1, probability = 0.8)
jncPairs.altDon <- findJunctionPairs(wds.altDon, type = "AD")
transcripts.altDon <- replaceJunction(wds.altDon, jncPairs.altDon, exons, type = "AD")

wds.altFirst <- filterWhippetEvents(wds, eventTypes = "AF", psiDelta = 0.1, probability = 0.8)
jncPairs.altFirst <- findJunctionPairs(wds.altFirst, type = "AF")
transcripts.altFirst <- replaceJunction(wds.altFirst, jncPairs.altFirst, exons, type = "AF")

wds.altLast <- filterWhippetEvents(wds, eventTypes = "AL", psiDelta = 0.1, probability = 0.8)
jncPairs.altLast <- findJunctionPairs(wds.altLast, type = "AL")
transcripts.altLast <- replaceJunction(wds.altLast, jncPairs.altLast, exons, type = "AL")

betsig/GeneStructureTools documentation built on March 31, 2021, 4:43 a.m.