MutationDefinition-class: S4 class defining replacement and silent mutation definitions

In shazam: Immunoglobulin Somatic Hypermutation Analysis

S4 class defining replacement and silent mutation definitions

Description

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

Slots

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.

See Also

See MUTATION_SCHEMES for a set of predefined MutationDefinition objects.

shazam documentation built on Nov. 5, 2025, 5:43 p.m.