getOrfs {GeneStructureTools} | R Documentation

## Get open reading frames for transcripts

### Description

Get open reading frames for transcripts

### Usage

    getOrfs(transcripts, BSgenome = NULL, returnLongestOnly = TRUE,
      allFrames = FALSE, longest = 1, exportFasta = FALSE, fastaFile = NULL,
      uORFs = FALSE)

### Arguments

`transcripts` | GRanges object with ONLY exon annotations (no gene, transcript, CDS etc.) with all transcripts for orf retrevial
`BSgenome` | BSgenome object
`returnLongestOnly` | only return longest ORF?
`allFrames` | return longest ORF for all 3 frames?
`longest` | return x longest ORFs (regardless of frames)
`exportFasta` | export a .fa.gz file with nucleotide sequences for each transcript?
`fastaFile` | file name for .fa.gz export
`uORFs` | get uORF summaries?

### Value

data.frame with longest orf details

### Author(s)

Beth Signal

### See Also

Other ORF annotation: `getUOrfs`, `maxLocation`, `orfSimilarity`

### Examples

    gtf <- rtracklayer::import(system.file("extdata", "example_gtf.gtf",
    package="GeneStructureTools"))
    transcript <- gtf[gtf$type=="exon" & gtf$gene_name=="Neurl1a"]
    g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
    # longest ORF for each transcripts
    orfs <- getOrfs(transcript, BSgenome = g, returnLongestOnly = TRUE)
    # longest ORF in all 3 frames for each transcript
    orfs <- getOrfs(transcript, BSgenome = g, allFrames = TRUE)
    # longest 3 ORFS in eacht transcript
    orfs <- getOrfs(transcript, BSgenome = g, returnLongestOnly = FALSE, longest=3)

[Package GeneStructureTools version 1.2.1 Index]