getOrfs {GeneStructureTools} | R Documentation |
Get open reading frames for transcripts
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)