getUOrfs: Get upstream open reading frames for transcripts with...

In betsig/GeneStructureTools: Tools for spliced gene structure manipulation and analysis

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", "gencode.vM25.small.gtf",
    package = "GeneStructureTools"
))
transcript <- gtf[gtf$type == "exon" & gtf$gene_name == "Tmem208"]
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)

betsig/GeneStructureTools documentation built on March 31, 2021, 4:43 a.m.