irfTranscriptChangeSummary: 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

irfTranscriptChangeSummary(
  irfDataSet,
  exons = NULL,
  BSgenome,
  intronMatchType = "exact",
  NMD = TRUE,
  exportGTF = NULL
)

Arguments

irfDataSet	irfsDataSet generated from readIrfDataSet()
exons	GRanges gtf annotation of exons
BSgenome	BSGenome object containing the genome for the species analysed
intronMatchType	what type of matching to perform in findIntronContainingTranscripts?
NMD	Use NMD predictions?
exportGTF	file name to export alternative isoform GTFs (default=NULL)

Value

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

Author(s)

Beth Signal

See Also

Other IRFinder data processing: filterIrfEvents(), readIrfDataSet()

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

irfinder_file <- list.files(system.file("extdata", "irf_small/", package = "GeneStructureTools"), full.names = TRUE)
irf <- readIrfDataSet(irfinder_file)
irf.filtered <- filterIrfEvents(irf, FDR = 0.01, psiDelta = 0.1)
irf_summary <- irfTranscriptChangeSummary(irf.filtered, exons, BSgenome = g)

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