whippetTranscriptChangeSummary {GeneStructureTools} | R Documentation

## Compare open reading frames for whippet differentially spliced events

### Description

Compare open reading frames for whippet differentially spliced events

### Usage

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

### Arguments

`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)

### 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

    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)

[Package GeneStructureTools version 1.14.0 Index]