MutationDefinition-class

MutationDefinition

<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 analyzing mutations in
immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of
antigen-driven selection pressure, mutational load quantification, building of
somatic hypermutation (SHM) models, and model-dependent distance calculations.
Also includes empirically derived models of SHM for both mice and humans.
Citations:
Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>,
Yaari, et al (2012) <doi:10.1093/nar/gks457>,
Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>,
Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.

Susanna Marquez

shazam

Immunoglobulin Somatic Hypermutation Analysis

Mohamed Uduman

Namita Gupta

Julian Zhou

Nima Nouri

Noah Yann Lee

Ang Cui

Jason Vander Heiden

Gur Yaari

Steven Kleinstein

MutationDefinition-class function

<dl>
<dt><code>name</code></dt>
<dd>name of the MutationDefinition.</dd></dl>
<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>

Slots

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

<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>

S4 class defining replacement and silent mutation definitions

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

Description

Arguments

Slots

See Also