whippetTranscriptChangeSummary: Compare open reading frames for whippet differentially...

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

Description

Compare open reading frames for whippet differentially spliced events

Usage

whippetTranscriptChangeSummary(
  whippetDataSet,
  unfilteredWDS,
  BSgenome,
  eventTypes = "all",
  exons,
  NMD = FALSE,
  exportGTF = NULL,
  selectLongest = 1
)

Arguments

whippetDataSet	whippetDataSet generated from readWhippetDataSet()
unfilteredWDS	unfiltered whippetDataSet generated from readWhippetDataSet() Note that this should contain ALL TS/TE events, regardless of significance, as these are used to construct the entire exon range.
BSgenome	BSGenome object containing the genome for the species analysed
eventTypes	which event type to filter for? default = "all"
exons	GRanges gtf annotation of exons
NMD	Use NMD predictions? (Note: notNMD must be installed to use this feature)
exportGTF	file name to export alternative isoform GTFs (default=NULL)
selectLongest	passed to getORFs()

Value

data.frame containing signficant whippet diff data and ORF change summaries

Author(s)

Beth Signal

See Also

Other whippet data processing: coordinates(), diffSplicingResults(), filterWhippetEvents(), formatWhippetEvents(), junctions(), readCounts(), readWhippetDIFFfiles(), readWhippetDataSet(), readWhippetJNCfiles(), readWhippetPSIfiles()

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

whippetFiles <- system.file("extdata", "whippet_small/",
    package = "GeneStructureTools"
)
wds.all <- readWhippetDataSet(whippetFiles)
wds.signif <- filterWhippetEvents(wds.all)
whippetTranscriptChangeSummary(whippetDataSet = wds.signif, unfilteredWDS = wds.all, exons = exons, BSgenome = g)

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