conserved_regions: Conserved and Non-conserved Regions from a MSA

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

Conserved and Non-conserved Regions from a MSA

Description

Returns the Conserved or the Non-conserved Regions from a MSA.

Usage

conserved_regions(x, ...)

## S4 method for signature 'Automorphism'
conserved_regions(
  x,
  conserved = TRUE,
  output = c("all_pairs", "unique_pairs", "unique")
)

## S4 method for signature 'AutomorphismList'
conserved_regions(
  x,
  conserved = TRUE,
  output = c("all_pairs", "unique_pairs", "unique"),
  num.cores = multicoreWorkers(),
  tasks = 0L,
  verbose = FALSE
)

## S4 method for signature 'AutomorphismByCoef'
conserved_regions(
  x,
  conserved = TRUE,
  output = c("all_pairs", "unique_pairs", "unique")
)

## S4 method for signature 'AutomorphismByCoefList'
conserved_regions(
  x,
  conserved = TRUE,
  output = c("all_pairs", "unique_pairs", "unique")
)

Arguments

x	A Automorphism-class, a AutomorphismList-class, a AutomorphismByCoef or a AutomorphismByCoefList class object.
...	Not in use.
conserved	Logical, Whether to return the conserved or the non-conserved regions.
output	A character string. Type of output.
num.cores, tasks	Integers. Argument num.cores denotes the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply function from BiocParallel package). Argument tasks denotes the number of tasks per job. value must be a scalar integer >= 0L. In this documentation a job is defined as a single call to a function, such as bplapply. A task is the division of the X argument into chunks. When tasks == 0 (default), X is divided as evenly as possible over the number of workers (see MulticoreParam from BiocParallel package).
verbose	logic(1). If TRUE, enable progress bar.

Value

A AutomorphismByCoef class object containing the requested regions.

Examples

## Load dataset
data("autm", package = "GenomAutomorphism")
conserved_regions(autm[1:3])
## Load automorphism found COVID datatset
data("covid_autm", package = "GenomAutomorphism")

## Conserved regions in the first 100 codons
conserv <- conserved_regions(covid_autm[1:100], output = "unique")
conserv

genomaths/GenomAutomorphism documentation built on Jan. 2, 2025, 12:25 a.m.