CodonSeq: A class definition to store codon coordinates given in the...

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

A class definition to store codon coordinates given in the Abelian group and the codon sequence.

Description

An objects from 'CodonSeq' or 'MatrixList' class is returned by function get_coord. This object will store the coordinate of each sequence in a list of 3D-vectors or a list of vectors located in the slot named 'CoordList'. The original codon sequence (if provided) will be stored in the slot named 'SeqRanges'.

Usage

coordList(x)

## S4 method for signature 'CodonSeq'
coordList(x)

seqRanges(x)

## S4 method for signature 'CodonSeq'
seqRanges(x)

Arguments

x	An object from CodonSeq-class.

Value

Given the slot values define a CodonSeq-class.

Examples

## Load a DNA sequence alignment 
data("aln", package = "GenomAutomorphism")

## Get base coordinates on 'Z5'
coord <- get_coord(
    x = aln,
    cube = "ACGT",
    group = "Z5"
)
coordList(coord)
## Load a DNA sequence alignment
data("aln", package = "GenomAutomorphism")

## Get base coordinates on 'Z5'
coord <- get_coord(
    x = aln,
    cube = "ACGT",
    group = "Z5"
)

seqRanges(coord)

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