Automorphism: A class definition to store codon automorphisms in a given...

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

A class definition to store codon automorphisms in a given Abelian group representation.

Description

Two classes are involved in to storing codon automorphisms: Automorphism-class and AutomorphismList-class.

Details

An Automorphism-class object has six columns: "seq1", "seq2","coord1", "coord2", "autm", and "cube". See the examples for function automorphisms. Observe that as the Automorphism-class inherits from GRanges-class the transformation starting from a GRanges-class object into an Automorphism-class is straightforward.

However, the transformation starting from a data.frame or a DataFrame-class object "x" requires for the creation of an additional GRanges-class object, which by default will have the argument seqnames = "1", strand = "+", start/end = seq(row(x)), length = nrow(x). These details must be keep in mind to prevent fundamental errors in the downstream analyses.

Value

Given the slot values, it defines an Automorphism-class object.

Automorphism-class methods

as(from, "Automorphism"):

Permits the transformation of a data.frame or a DataFrame-class object into Automorphism-class object if the proper columns are provided.

Methods from GRanges-class can also be applied.

See Also

AutomorphismByCoef-class and AutomorphismList-class

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