getOrfs: Get open reading frames for transcripts

Description Usage Arguments Value Author(s) See Also Examples

View source: R/longestORF.R

Description

Get open reading frames for transcripts

Usage

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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

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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.