CodonMatrix: A Convenient Class to Store a Codon Coordinate in given...

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

A Convenient Class to Store a Codon Coordinate in given Genetic Code cube.

Description

A CodonMatrix is the object created by function codon_matrix

Usage

CodonMatrix(object, group, cube, seq_alias = NULL)

Arguments

object	A GRanges-class object.
group	The name of the base group, 'Z4' or 'Z5'.
cube	The name of the genetic-code cube applied to get the codon coordinates.
seq_alias	The 'alias' given to the codon sequence.

Value

A 'CodonMatrix' class object

See Also

base_coord and codon_coord.

Examples

## CodonMatrix is generated by function 'codon_matrix' (inside a
## ListCodonMatrix-class object)
## Let's create DNAStringSet-class object
base <- DNAStringSet(x = c(S1 = 'ACGTGATCAAGT'))

x1 <- codon_matrix(base)
x1

## Extract the first element
x1[1]
x1$codon.1
x1[[1]]

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