getUOrfs {GeneStructureTools} | R Documentation

## Get upstream open reading frames for transcripts with annotated main ORFs

### Description

Get upstream open reading frames for transcripts with annotated main ORFs

### Usage

    getUOrfs(transcripts, BSgenome = NULL, orfs, findExonB = FALSE)

### Arguments

`transcripts` | GRanges object with ONLY exon annotations (no gene, transcript, CDS etc.) with all transcripts for orf retrevial
`BSgenome` | BSgenome object
`orfs` | orf annotation for the transcripts object. Generated by getOrfs(transcripts, ...)
`findExonB` | find the distance to and exon number of the downstream (B) junction?

### Value

data.frame with all upstream ORF details.

### Author(s)

Beth Signal

### See Also

Other ORF annotation: `getOrfs`, `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 = FALSE)
    uORFS <- getUOrfs(transcript, BSgenome = g, orfs = orfs, findExonB = TRUE)

[Package GeneStructureTools version 1.14.0 Index]