| getUOrfs {GeneStructureTools} | R Documentation |
Get upstream open reading frames for transcripts with annotated main ORFs
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)