dna_phychem: DNA numerical matrix

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

DNA numerical matrix

Description

This function applies the numerical indices representing various physicochemical and biochemical properties of DNA bases. As results, DNA sequences are represented as numerical vectors which can be subject of further downstream statistical analysis and digital signal processing.

Usage

dna_phychem(seqs, ...)

## S4 method for signature 'character'
dna_phychem(
  seqs,
  phychem = list(A = NULL, T = NULL, C = NULL, G = NULL, N = NULL)
)

## S4 method for signature 'DNAStringSet_OR_DNAMultipleAlignment'
dna_phychem(
  seqs,
  phychem = list(A = NULL, T = NULL, C = NULL, G = NULL, N = NULL),
  index_name = NULL,
  ...
)

Arguments

seqs	A character string, a DNAStringSet or a DNAMultipleAlignment class object carrying the DNA pairwise alignment of two sequences.
...	Not in use.
phychem	A list of DNA bases physicochemical properties, e.g., like those provided in dna_phyche.
index_name	Optional. Name of breve description of the base physicochemical property applied to represent the DNA sequence.

Value

A MatrixSeq-class object.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

peptide_phychem_index

Examples

## Let's create DNAStringSet-class object 
base <- DNAStringSet(x = c( seq1 ='ACGTGATCAAGT', 
                            seq2 = 'GTGTGATCCAGT', 
                            seq3 = 'TCCTGATCAGGT'))


dna_phychem(seqs = base,
            phychem = list('A' = 0.87, 'C' = 0.88, 'T' = 0.82,
                            'G' = 0.89, 'N' = NA),
            index_name = "Proton-Affinity")

genomaths/GenomAutomorphism documentation built on May 10, 2024, 12:11 a.m.