automorphismByRanges: Get the automorphisms by ranges.

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

Get the automorphisms by ranges.

Description

Automorphisms estimated on a pairwise or a MSA alignment can be grouped by ranges which inherits from GRanges-class or a GRanges-class.

Usage

automorphismByRanges(x, ...)

## S4 method for signature 'Automorphism'
automorphismByRanges(x)

## S4 method for signature 'AutomorphismList'
automorphismByRanges(
  x,
  min.len = 0L,
  num.cores = multicoreWorkers(),
  tasks = 0L,
  verbose = TRUE
)

Arguments

x	An AutomorphismList-class object returned by function automorphisms.
...	Not in use.
min.len	Minimum length of a range to be reported.
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 GRanges-class or a GRangesList-class. Each GRanges-class object with a column named cube, which carries the type of cube automorphims.

Examples

## Load dataset
data("autm", package = "GenomAutomorphism")

automorphismByRanges(x = autm[c(1, 4)])

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