altSpliceSiteRmats: Generate isoforms with different 5' or 3' splice site usage...

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

Description

Generate isoforms with different 5' or 3' splice site usage from RMATS data

Usage

altSpliceSiteRmats(rmatsEvents, exons, eventType)

Arguments

rmatsEvents	data.frame containing RMATS RI events
exons	reference exons GRanges
eventType	type of event. "A5E" - alternative 5', or "A3E" - alternative 3'

Value

GRanges of isoforms

Author(s)

Beth Signal

See Also

Other rmats data processing: altIntronRmats(), 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.A5E <- extractEvent(rds.filtered, "A5SS")
isoforms.A5E <- altSpliceSiteRmats(diffSplice.A5E, exons = exons, eventType = "A5SS")

diffSplice.A3E <- extractEvent(rds.filtered, "A3SS")
isoforms.A3E <- altSpliceSiteRmats(diffSplice.A3E, exons = exons, eventType = "A3SS")

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