R: S4 class defining replacement and silent mutation definitions

MutationDefinition-class {shazam}

R Documentation

S4 class defining replacement and silent mutation definitions

MutationDefinition defines a common data structure for defining the whether a mutation is annotated as a replacement or silent mutation.

name: name of the MutationDefinition.
description: description of the model and its source.
classes: named character vectors with single-letter amino acid codes as names and amino acid classes as values, with NA assigned to set of characters c("X", "*", "-", "."). Replacement (R) is be defined as a change in amino acid class and silent (S) as no change in class.
codonTable: matrix of codons (columns) and substitutions (rows).
citation: publication source.