cdm_z64: Codon Distance Matrices for the Standard Genetic Code on Z4

In genomaths/GenomAutomorphism: Compute the automorphisms between DNA's Abelian group representations

Codon Distance Matrices for the Standard Genetic Code on Z4

Description

This is a list of 24 codon distance matrices created with function codon_dist_matrix in the set of 24 genetic-code cubes on Z4 (using the default weights and assuming the standard genetic code (SGC). The data set is created to speed up the computation when working with DNA sequences from superior organisms. Since distance matrices are symmetric, it is enough to provide the lower matrix. Each matrix is given as named/labeled vector (see the example).

Usage

data("cdm_z64", package = "GenomAutomorphism")

Format

A list object.

Examples

## Load the data set
data("cdm_z64", package = "GenomAutomorphism")
cdm_z64

## The lower matrix (given as vector) for cube "TCGA" (picking out the 20 
## first values). Observe that this vector is labeled. Each numerical value 
## corresponds to the distance between the codons specified by the 
## name/label on it. For example, the distance between codons TTT and TCT 
## is: 0.0625.

head(cdm_z64[[ "TCGA" ]], 20)

genomaths/GenomAutomorphism documentation built on Dec. 12, 2024, 2:12 p.m.