AutomorphismList: A class definition to store list of Automorphism class...

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

A class definition to store list of Automorphism class objects.

Description

A class definition to store list of Automorphism class objects derived from the pairwise automorphism estimation from pairwise alignments. Objects from this class are created by function automorphisms and as.AutomorphismList.

Usage

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

## S4 replacement method for signature 'AutomorphismList,ANY'
names(x) <- value

## S4 method for signature 'AutomorphismList'
as.list(x)

## S4 method for signature 'AutomorphismList'
show(object)

Arguments

x	An AutomorphismList-class object.
value	A character vector naming the elements of the AutomorphismList-class object 'x'.
object	An object from AutomorphismList-class.

Value

An object from AutomorphismList-class

AutomorphismList-class methods

as.AutomorphismList(x):

as.AutomorphismList function transform a list of GRanges-class, a GRangesList-class, a list of data.frame or a DataFrame-class objects into a AutomorphismList-class object.

unlist(x)

It transforms a AutomorphismList-class object into an Automorphism-class object.

as.list(x)

It transforms a list of Automorphism-class objects into an AutomorphismList-class object.

as(x, "GRangesList")

It transforms a GRangesList of Automorphism-class objects into an 'AutomorphismList-class' object.

names(x)

To get the element's names from an 'AutomorphismList-class' object.

names(x) <- value

To assign names to the element from an 'AutomorphismList-class' object.

See Also

Automorphism-class and AutomorphismByCoefList-class.

Examples

## Load datasets
data("autm", "brca1_autm")

## Transforming a list of Automorphisms into an AutomorphismList object
lista <- list(human = brca1_autm[[1]], gorilla = brca1_autm[[2]])
as.AutomorphismList(lista)

## Alternatively we can set
aut <- as.list(brca1_autm[seq(2)])
class(aut)

## And reverse it
aut <- as.AutomorphismList(aut)
aut

## Let's get the element names from object 'aut'
names(aut)

## Let's assign new names
names(aut) <- c("human_1", "gorilla_1")
names(aut)

## Transforming a GRangesList of Automorphisms into an AutomorphismList
## object
lista <- as(lista, "GRangesList")
as.AutomorphismList(lista)

## Transform a AutomorphismList-class object into an Automorphism-class
## object 
unlist(brca1_autm[seq(2)])
## Load a DNA sequence alignment
data("brca1_autm", package = "GenomAutomorphism")
names(brca1_autm)
## Load a DNA sequence alignment
data("brca1_autm", package = "GenomAutomorphism")
x1 <- brca1_autm[seq(2)]
names(x1)

## Let's assign a new names
names(x1) <- c("human_1.human_2.0", "human_1.gorilla_0")
names(x1) 
## Load a DNA sequence alignment
data("brca1_autm", package = "GenomAutomorphism")

## The list of the first three elements
autm_list <- as.list(brca1_autm[seq(3)])
autm_list

genomaths/GenomAutomorphism documentation built on April 29, 2024, 4:31 p.m.