getOrfs: Get open reading frames for transcripts

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

Description

Get open reading frames for transcripts

Usage

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

Arguments

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?
selectLongest	proportion of ORFs for each gene to find uORFs for. Value between 0 and 1. Speeds up uORF calculations but will only return results for the longest ORFs.

Value

data.frame with longest orf details

Author(s)

Beth Signal

See Also

Other ORF annotation: getUOrfs(), 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 = 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)

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