leafcutterTranscriptChangeSummary {GeneStructureTools} | R Documentation

## Compare open reading frames for whippet differentially spliced events

### Description

Compare open reading frames for whippet differentially spliced events

### Usage

    leafcutterTranscriptChangeSummary(significantEvents,
      combineGeneEvents = FALSE, exons, BSgenome, NMD = FALSE,
      showProgressBar = TRUE, exportGTF = NULL)

### Arguments

`significantEvents` | data.frame containing information from the per_intron_results.tab file output from leafcutter.
`combineGeneEvents` | combine clusters occuring in the same gene? Currently not reccomended.
`exons` | GRanges gtf annotation of exons
`BSgenome` | BSGenome object containing the genome for the species analysed
`NMD` | Use NMD predictions? (Note: notNMD must be installed to use this feature)
`showProgressBar` | show a progress bar of alternative isoform generation?
`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

### Examples

    leafcutterFiles <- list.files(system.file("extdata","leafcutter/",
    package = "GeneStructureTools"), full.names = TRUE)
    leafcutterIntrons <- read.delim(leafcutterFiles[
    grep("intron_results", leafcutterFiles)],stringsAsFactors=FALSE)
    gtf <- rtracklayer::import(system.file("extdata","example_gtf.gtf",
    package = "GeneStructureTools"))
    exons <- gtf[gtf$type=="exon"]
    g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
    leafcutterTranscriptChangeSummary(significantEvents = leafcutterIntrons,
    exons=exons,BSgenome = g,NMD=FALSE)

[Package GeneStructureTools version 1.2.1 Index]