whippetTranscriptChangeSummary: Compare open reading frames for whippet differentially...
In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description Usage Arguments Value Author(s) See Also Examples

Compare open reading frames for whippet differentially spliced events

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whippetTranscriptChangeSummary(whippetDataSet, gtf.all = NULL, BSgenome,
  eventTypes = "all", exons = NULL, transcripts = NULL, NMD = FALSE,
  exportGTF = NULL)

`whippetDataSet`	whippetDataSet generated from `readWhippetDataSet()`
`gtf.all`	GRanges gtf annotation (can be used instead of specifying exons and transcripts)
`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
`transcripts`	GRanges gtf annotation of transcripts
`NMD`	Use NMD predictions? (Note: notNMD must be installed to use this feature)
`exportGTF`	file name to export alternative isoform GTFs (default=NULL)

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

Beth Signal

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

whippetFiles <- system.file("extdata","whippet/",
package = "GeneStructureTools")
wds <- readWhippetDataSet(whippetFiles)
wds <- filterWhippetEvents(wds)

gtf <- rtracklayer::import(system.file("extdata","example_gtf.gtf",
package = "GeneStructureTools"))
g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
whippetTranscriptChangeSummary(wds, gtf.all=gtf,BSgenome = g)