artificial.from.cds: Artificial ORFs from CDS
In Roleren/uORFomePipe: uORF prediction in R

artificial.from.cds

R Documentation

Artificial ORFs from CDS

Description

A wrapper to ORFik:::artificial.orfs, that create artificial ORFs from CDS, with given start and stop codons of size size * 6

Usage

artificial.from.cds(
  cds,
  size = 100,
  startCodons = c("ATG", "CTG", "TTG", "AAG", "AGG"),
  stopCodons = c("TAA", "TGA", "TAG"),
  fa,
  mode = "aCDS"
)

Arguments

`cds`	GRangesList of CDS
`size`	integer, default: 100, 1/6 of maximum size of ORFs (max size 600 if 100)
`startCodons,`	character vector, default: c("ATG", "CTG", "TTG", "AAG", "AGG")
`stopCodons`	character vector, default: c("TAA", "TGA", "TAG")
`fa`	a FaFile or path to fasta index file
`mode`	character, default: "aCDS", must be either CDS or aCDS (artificial CDS)