getOrfs: Get open reading frames for transcripts
In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description Usage Arguments Value Author(s) See Also Examples

Get open reading frames for transcripts

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getOrfs(transcripts, BSgenome = NULL, returnLongestOnly = TRUE,
  allFrames = FALSE, longest = 1, exportFasta = FALSE, fastaFile = NULL,
  uORFs = FALSE)

`transcripts`	GRanges object with ONLY exon annotations (no gene, transcript, CDS etc.) with all transcripts for orf retrevial
`BSgenome`	BSgenome object
`returnLongestOnly`	only return longest ORF?
`allFrames`	return longest ORF for all 3 frames?
`longest`	return x longest ORFs (regardless of frames)
`exportFasta`	export a .fa.gz file with nucleotide sequences for each transcript?
`fastaFile`	file name for .fa.gz export
`uORFs`	get uORF summaries?

data.frame with longest orf details

Beth Signal

Other ORF annotation: getUOrfs, 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 = TRUE)
# longest ORF in all 3 frames for each transcript
orfs <- getOrfs(transcript, BSgenome = g, allFrames = TRUE)
# longest 3 ORFS in eacht transcript
orfs <- getOrfs(transcript, BSgenome = g, returnLongestOnly = FALSE, longest=3)