skipExonByJunction: Generate isoforms with and without a skipped exon (or...

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

Description

Generate isoforms with and without a skipped exon (or mutually exclusive exons)

Usage

skipExonByJunction(rmatsEvents, eventType = "SE", exons)

Arguments

rmatsEvents	data.frame containing RMATS SE or MXE events
eventType	type of event to skip exons for. "SE" - skipped exons, or "MXE" - mutually exclusive exons
exons	reference exons GRanges

Value

data.frame with overlapping event/exons

Author(s)

Beth Signal

See Also

Other rmats data processing: altIntronRmats(), altSpliceSiteRmats(), annotateEventCoords(), annotateOverlapRmats(), betweenNumbers(), duplicateReference(), exonsToIntrons(), extractEvent(), filterRmatsEvents(), readRmatsDataSet(), reformatExons(), removeDuplicatePairs(), removeExonsBetween(), rmatsTranscriptChangeSummary(), splitLongExons()

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

rmats_directory <- system.file("extdata", "rmats_small/", package = "GeneStructureTools")
rds <- readRmatsDataSet(rmats_directory)
rds.filtered <- filterRmatsEvents(rds, FDR = 0.01, psiDelta = 0.1)

diffSplice.MXE <- extractEvent(rds.filtered, "MXE")
isoforms.MXE <- skipExonByJunction(diffSplice.MXE, eventType = "MXE", exons = exons)

diffSplice.SE <- extractEvent(rds.filtered, "SE")
isoforms.SE <- skipExonByJunction(diffSplice.SE, eventType = "SE", exons = exons)

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