rmatsTranscriptChangeSummary: Compare open reading frames for RMATS differentially spliced...

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

Description

Compare open reading frames for RMATS differentially spliced events

Usage

rmatsTranscriptChangeSummary(
  rmatsDataSet,
  exons = NULL,
  eventTypes = "all",
  BSgenome,
  NMD = TRUE,
  exportGTF = NULL
)

Arguments

rmatsDataSet	rmatsDataSet generated from readRmatsDataSet()
exons	GRanges gtf annotation of exons
eventTypes	which event type to filter for? default="all"
BSgenome	BSGenome object containing the genome for the species analysed
NMD	Use NMD predictions? (Note: notNMD must be installed to use this feature)
exportGTF	file name to export alternative isoform GTFs (default=NULL)

Value

data.frame containing significant RMATS differential splicing data and ORF change summaries

Author(s)

Beth Signal

See Also

Other rmats data processing: altIntronRmats(), altSpliceSiteRmats(), annotateEventCoords(), annotateOverlapRmats(), betweenNumbers(), duplicateReference(), exonsToIntrons(), extractEvent(), filterRmatsEvents(), readRmatsDataSet(), reformatExons(), removeDuplicatePairs(), removeExonsBetween(), 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)
rmats_summary <- rmatsTranscriptChangeSummary(rmatsDataSet = rds.filtered, exons, BSgenome = g)

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