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 1.12.0 Index]