codon_matrix: Codon Coordinate Matrix

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

Codon Coordinate Matrix

Description

This function build the coordinate matrix for each sequence from an aligned set of DNA codon sequences.

Usage

codon_matrix(base, ...)

## S4 method for signature 'BaseSeqMatrix'
codon_matrix(base, num.cores = 1L, tasks = 0L, verbose = TRUE, ...)

## S4 method for signature 'DNAStringSet'
codon_matrix(
  base,
  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"),
  group = c("Z4", "Z5"),
  num.cores = 1L,
  tasks = 0L,
  verbose = TRUE
)

## S4 method for signature 'DNAMultipleAlignment'
codon_matrix(
  base,
  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"),
  group = c("Z4", "Z5"),
  num.cores = 1L,
  tasks = 0L,
  verbose = TRUE
)

Arguments

base	A DNAMultipleAlignment, a DNAStringSet, or a BaseSeqMatrix.
...	Not in use yet.
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the function log to stdout
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (3-4).
group	A character string denoting the group representation for the given base or codon as shown in reference (3-4).

Details

The purpose of this function is making the codon coordinates from multiple sequence alignments (MSA) available for further downstream statistical analyses, like those reported in references (1) and (2).

Value

A ListCodonMatrix class object with the codon coordinate on its metacolumns.

Author(s)

Robersy Sanchez https://genomaths.com

References

1. Lorenzo-Ginori, Juan V., Aníbal Rodríguez-Fuentes, Ricardo Grau Ábalo, and Robersy Sánchez Rodríguez. "Digital signal processing in the analysis of genomic sequences." Current Bioinformatics 4, no. 1 (2009): 28-40.

2. Sanchez, Robersy. "Evolutionary analysis of DNA-protein-coding regions based on a genetic code cube metric." Current Topics in Medicinal Chemistry 14, no. 3 (2014): 407-417.

3. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi: 10.1101/2021.06.01.446543

4. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.

5. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560.

See Also

codon_coord, base_coord and base2int.

Examples

## Load the MSA of Primate BRCA1 DNA repair genes
data("brca1_aln")

## Get the DNAStringSet for the first 33 codons and apply 'codon_matrix'
brca1 <- unmasked(brca1_aln)
brca1 <- subseq(brca1, start = 1, end = 33)
codon_matrix(brca1)

## Get back the alignment object and apply 'codon_matrix' gives us the 
## same result.
brca1 <- DNAMultipleAlignment(as.character(brca1))
codon_matrix(brca1)

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