codon_dist_matrix: Compute Codon Distance Matrix

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

Compute Codon Distance Matrix

Description

This function computes the codon distance matrix based on the weighted Manhattan distance between codons estimated with function codon_dist.

Usage

codon_dist_matrix(
  genetic_code = "1",
  group = c("Z4", "Z5"),
  weight = NULL,
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  output = c("list", "vector", "dist"),
  num.cores = 1L
)

Arguments

genetic_code	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.
group	A character string denoting the group representation for the given codon sequence as shown in reference (2-3).
weight	A numerical vector of weights to compute weighted Manhattan distance between codons. If weight = NULL, then weight = (1/4,1,1/16) for group = "Z4" and weight = (1/5,1,1/25) for group = "Z5" (see codon_dist).
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (2-3).
output	Format of the returned lower triangular matrix: as a list of 63 elements (labeled) or as a labeled vector using codons as labels.
num.cores	An integer to setup the number of parallel workers via makeCluster.

Details

By construction, a distance matrix is a symmetric matrix. Hence, the knowledge of lower triangular matrix is enough for its application to any downstream analysis.

Value

A lower triangular matrix excluding the diagonal.

See Also

codon_dist.

Examples

## The distance matrix for codons for the Invertebrate Mitochondrial,
## cube "TGCA" with base-triplet represented on the group "Z5". Each 
## coordinate from each returned numerical vector corresponds to the 
## distance between codons given in the coordinate name. 
x <- codon_dist_matrix(genetic_code = "5", cube = "TGCA", group = "Z5",
                    output = "vector")
x[seq(61, 63)]

genomaths/GenomAutomorphism documentation built on April 29, 2024, 4:31 p.m.