transcriptChangeSummary {GeneStructureTools} | R Documentation

## Compare open reading frames for two sets of paired transcripts

### Description

Compare open reading frames for two sets of paired transcripts

### Usage

    transcriptChangeSummary(transcriptsX, transcriptsY, BSgenome, exons,
      NMD = FALSE, NMDModel = NULL, compareBy = "gene",
      orfPrediction = "allFrames", compareToGene = FALSE,
      whippetDataSet = NULL, exportGTF = NULL)

### Arguments

`transcriptsX` | GRanges object with exon annotations for all transcripts to be compared for the 'normal' condition
`transcriptsY` | GRanges object with exon annotations for all transcripts to be compared for the 'alternative' condition
`BSgenome` | BSGenome object containing the genome for the species analysed
`exons` | GRanges object made from a GTF containing exon coordinates
`NMD` | Use NMD predictions? (Note: notNMD must be installed to use this feature)
`NMDModel` | Use the "base" or "lncRNA" NMD model?
`compareBy` | compare isoforms by 'transcript' id, or aggregate all changes occuring by 'gene'
`orfPrediction` | What type of orf predictions to return. default= `"allFrames"`
`compareToGene` | compare alternative isoforms to all normal gene isoforms (in exons)
`whippetDataSet` | whippetDataSet generated from `readWhippetDataSet()` Use if PSI directionality should be taken into account when comparing isoforms.
`exportGTF` | file name to export alternative isoform GTFs (default=`NULL`)

### Value

Summarised ORF changes data.frame

### Author(s)

Beth Signal

### See Also

Other transcript isoform comparisons: `attrChangeAltSpliced`, `orfDiff`

### 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"))
    exons <- gtf[gtf$type=="exon"]
    g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10

    wds.exonSkip <- filterWhippetEvents(wds, eventTypes="CE",psiDelta = 0.2)

    exons.exonSkip <- findExonContainingTranscripts(wds.exonSkip, exons,
    variableWidth=0, findIntrons=FALSE, transcripts)
    ExonSkippingTranscripts <- skipExonInTranscript(exons.exonSkip, exons, whippetDataSet=wds.exonSkip)
    transcriptChangeSummary(ExonSkippingTranscripts[ExonSkippingTranscripts$set=="included_exon"],
    ExonSkippingTranscripts[ExonSkippingTranscripts$set=="skipped_exon"],
    BSgenome=g,exons)

[Package GeneStructureTools version 1.4.0 Index]