attrChangeAltSpliced {GeneStructureTools} | R Documentation

## Evaluate the change in an attribute between a set of 'normal' transcripts and 'alternative' transcripts

### Description

Evaluate the change in an attribute between a set of 'normal' transcripts and 'alternative' transcripts

### Usage

    attrChangeAltSpliced(orfsX, orfsY, attribute = "orf_length",
      compareBy = "gene", useMax = TRUE, compareUTR = FALSE)

### Arguments

`orfsX` | orf information for 'normal' transcripts. Generated by getOrfs()
`orfsY` | orf information for 'alternative' transcripts. Generated by getOrfs()
`attribute` | attribute to compare
`compareBy` | compare by 'transcript' isoforms or by 'gene' groups
`useMax` | use max as the summary function when multiple isoforms are aggregated? If FALSE, will use min instead.
`compareUTR` | compare the UTR lengths between transcripts? Only runs if attribute = "orf_length"

### Value

data.frame with attribute changes

### Author(s)

Beth Signal

### See Also

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

### 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$type=="exon"]
    transcripts <- gtf[gtf$type=="transcript"]
    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)

    orfsSkipped <- getOrfs(ExonSkippingTranscripts[ExonSkippingTranscripts$set=="skipped_exon"],
    BSgenome = g)
    orfsIncluded <- getOrfs(ExonSkippingTranscripts[ExonSkippingTranscripts$set=="included_exon"],
    BSgenome = g)
    attrChangeAltSpliced(orfsSkipped, orfsIncluded,attribute = "orf_length")

[Package GeneStructureTools version 1.2.1 Index]