automorphism_bycoef: Autmorphism Grouping by Coefficient

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

Autmorphism Grouping by Coefficient

Description

Automorphisms with the same automorphism's coefficients are grouped.

Usage

automorphism_bycoef(x, ...)

## S4 method for signature 'Automorphism'
automorphism_bycoef(x, mut.type = TRUE)

## S4 method for signature 'AutomorphismList'
automorphism_bycoef(
  x,
  min.len = 1L,
  mut.type = TRUE,
  num.cores = multicoreWorkers(),
  tasks = 0L,
  verbose = TRUE
)

Arguments

x	An automorphism-class object returned by function automorphisms.
...	Not in use.
mut.type	Logical. Whether to include the mutation type as given by function mut_type.
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

An AutomorphismByCoef class object. A coefficient with 0 value is assigned to mutational events that are not automorphisms, e.g., indel mutations.

See Also

automorphisms

Examples

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

automorphism_bycoef(x = autm[1:2])

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