A class definition to store codon automorphisms in a given Abelian group representation.
Source:R/allClasses.R
Automorphism.RdTwo 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.
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.