altIntronRmats: Generate isoforms with and without a retain intron from RMATS...

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

Description

Generate isoforms with and without a retain intron from RMATS data shortcut function: uses the same base function for intron retention

Usage

altIntronRmats(rmatsEvents, exons)

Arguments

rmatsEvents	data.frame containing RMATS RI events
exons	reference exons GRanges

Value

GRanges retained and skipped intron isoforms

Author(s)

Beth Signal

See Also

Other rmats data processing: altSpliceSiteRmats(), annotateEventCoords(), annotateOverlapRmats(), betweenNumbers(), duplicateReference(), exonsToIntrons(), extractEvent(), filterRmatsEvents(), readRmatsDataSet(), reformatExons(), removeDuplicatePairs(), removeExonsBetween(), rmatsTranscriptChangeSummary(), skipExonByJunction(), 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.RI <- extractEvent(rds.filtered, "RI")
isoforms.RI <- altIntronRmats(diffSplice.RI, exons = exons)

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