subset.ORF: Subset orfs by filters given

In Roleren/uORFomePipe: uORF prediction in R

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.