getAutomorphisms: Get Automorphisms

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

Get Automorphisms

Description

For the sake of saving memory, each Automorphism-class objects is stored in an AutomorphismList-class, which does not inherits from a GRanges-class.

Usage

getAutomorphisms(x, ...)

## S4 method for signature 'AutomorphismList'
getAutomorphisms(x)

## S4 method for signature 'list'
getAutomorphisms(x)

## S4 method for signature 'DataFrame_OR_data.frame'
getAutomorphisms(x)

Arguments

x	An AutomorphismList-class.
...	Not in use.

Details

This function just transform each Automorphism-class object into an object from the same class but now inheriting from a GRanges-class.

Value

This function returns an AutomorphismList-class object as a list of Automorphism-class objects, which inherits from GRanges-class objects.

An AutomorphismList-class

An Automorphism-class

Examples

## Load a dataset
data("autm", package = "GenomAutomorphism")
aut <- mcols(autm)
aut ## This a DataFrame object

## The natural ranges for the sequence (from 1 to length(aut)) are added
getAutomorphisms(aut)

## A list of automorphisms
aut <- list(aut, aut)
getAutomorphisms(aut)

## Automorphism-class inherits from 'GRanges-class'
aut <- as(autm, "GRanges")
as(aut, "Automorphism")

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