genCode-class: An S4 class 'genCode'

In coRdon: Codon Usage Analysis and Prediction of Gene Expressivity

Description

Object of genCode class describes the variant of genetic code to be used in CU calculations.

Usage

genCode(id_or_name2 = "1", alt.init = TRUE, stop.rm = FALSE)

## S4 method for signature 'ANY'
genCode(id_or_name2 = "1", alt.init = TRUE,
  stop.rm = FALSE)

Arguments

id_or_name2	A single string that uniquely identifies the genetic code to extract. Should be one of the values in the id or name2 columns of GENETIC_CODE_TABLE.
alt.init	logical, whether to use alternative initiation codons. Default is TRUE.
stop.rm	logical, whether to remove stop codons. Default is FALSE.

Value

A genCode object.

Methods (by generic)

• genCode: Creates new instances of genCode class.

Slots

ctab

A data.table with two colums: codon and AA, amino acid.

codons

A character vector of codons.

stops

A character vector of stop codons. Note that, if stop.rm is TRUE, this will be an empty vector.

nostops

A character vector of no-stop codons. If stop.rm is TRUE, this will be equal to the codons slot.

cl

A list, each element of which is a vector of integers indicating the positions of synonymous codons for that amino acid, when codons are ordered alphabetically.

deg

A numeric vector of degeneracies for alphabetically ordered amino acids.

coRdon documentation built on Nov. 8, 2020, 5:28 p.m.