subset.ORF: Subset orfs by filters given

View source: R/Utils.R

subset.ORFR Documentation

Subset orfs by filters given

Description

Subset orfs by filters given

Usage

## S3 method for class 'ORF'
subset(
  orfs,
  minimum.length = 6,
  must.be.mod.3.0 = TRUE,
  startCodons = c("ATG", "CTG", "TTG"),
  stopCodons = c("TAA", "TGA", "TAG"),
  fa
)

Arguments

orfs

GRangesList of ORFs

minimum.length

numeric, default 6

must.be.mod.3.0

logical, default TRUE

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

Value

GRangesList of subset that is valid by filter


Roleren/uORFomePipe documentation built on Jan. 14, 2024, 5:11 a.m.