orfDiff {GeneStructureTools} | R Documentation

## Evaluate changes to ORFs caused by alternative splicing

### Description

Evaluate changes to ORFs caused by alternative splicing

### Usage

    orfDiff(orfsX, orfsY, filterNMD = TRUE, geneSimilarity = TRUE,
      compareUTR = TRUE, compareBy = "gene", allORFs = NULL)

### Arguments

`orfsX` | orf information for 'normal' transcripts. Generated by getOrfs()
`orfsY` | orf information for 'alternative' transcripts. Generated by getOrfs()
`filterNMD` | filter orf information for transcripts not targeted by nmd first?
`geneSimilarity` | compare orf to all orfs in gene?
`compareUTR` | compare UTRs?
`compareBy` | compare by 'transcript' isoforms or by 'gene' groups
`allORFs` | orf information for all transcripts for novel sequence comparisons. Generated by getOrfs()

### Value

data.frame with orf changes

### Author(s)

Beth Signal

### See Also

Other transcript isoform comparisons: `attrChangeAltSpliced`, `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

    orfsProteinCoding <- getOrfs(exons[exons$gene_name=="Prex2" &
    exons$transcript_type=="protein_coding"], BSgenome = g)
    orfsNMD <- getOrfs(exons[exons$gene_name=="Prex2" &
    exons$transcript_type=="nonsense_mediated_decay"], BSgenome = g)
    orfDiff(orfsProteinCoding, orfsNMD, filterNMD=FALSE)

    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)
    orfDiff(orfsSkipped, orfsIncluded, filterNMD=FALSE)

[Package GeneStructureTools version 1.4.0 Index]