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

In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

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

findJunctionPairs(whippetDataSet, jncCoords, type = NA)

Arguments

whippetDataSet	whippetDataSet generated from readWhippetDataSet()
jncCoords	GRanges object with Whippet junctions. Generated by readWhippetJNCfiles()
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, findExonContainingTranscripts, findIntronContainingTranscripts, 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$type=="exon"]
transcripts <- gtf[gtf$type=="transcript"]
g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10

wds.altAce <- filterWhippetEvents(wds, eventTypes="AA")
jncPairs.altAce <- findJunctionPairs(wds.altAce, type="AA")

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

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

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

GeneStructureTools documentation built on Nov. 8, 2020, 6:04 p.m.