getUOrfs: Get upstream open reading frames for transcripts with...
In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description Usage Arguments Value Author(s) See Also Examples

Get upstream open reading frames for transcripts with annotated main ORFs

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

`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?

data.frame with all upstream ORF details.

Beth Signal

Other ORF annotation: getOrfs, maxLocation, orfSimilarity

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)