findJunctionPairs: Find alternative junctions for Whippet alternative splicing...

Description Usage Arguments Value Author(s) See Also Examples

View source: R/AltSplicingJunctionSupported.R

Description

Find junctions that pair with each end of an AA (alt. acceptor) or AD (alt. donor) whippet range Find junctions that pair with the upsteam/downstream exon of an AF (alt. first exon) or an AL (alt. last exon)

Usage

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findJunctionPairs(whippetDataSet, type = NA)

Arguments

whippetDataSet

whippetDataSet generated from readWhippetDataSet()

type

type of Whippet event (AA/AD/AF/AL). Note only one event type should be processed at a time.

Value

GRanges object with alternative junctions. Each event should have a set of X (for which the psi measurement is reported) junctions, and alternative Y junctions.

Author(s)

Beth Signal

See Also

Other whippet splicing isoform creation: addIntronInTranscript(), alterTranscriptStartEnds(), findExonContainingTranscripts(), findIntronContainingTranscripts(), replaceJunction(), skipExonInTranscript()

Examples

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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")

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

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

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

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