MutationDefinition

MutationDefinition-class


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


Provides a computational framework for Bayesian estimation of
antigen-driven selection in immunoglobulin (Ig) sequences, providing an
intuitive means of analyzing selection by quantifying the degree of
selective pressure. Also provides tools to profile mutations in Ig
sequences, build models of somatic hypermutation (SHM) in Ig sequences,
and make model-dependent distance comparisons of Ig repertoires.

Jason Vander Heiden

shazam

Immunoglobulin Somatic Hypermutation Analysis

MutationDefinition-class function

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

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

Description

Arguments

Slots

See Also