MutabilityModel-class

MutabilityModel

print,MutabilityModel-method

MutabilityModel-method

as.data.frame,MutabilityModel-method

<code>MutabilityModel</code> defines a data structure for the 5-mer motif-based SHM targeting
mutability model.

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

MutabilityModel-class function

<dl><dt>x</dt>
<dd><code>MutabilityModel</code> object.</dd></dl>

Arguments

<dl>
<dt><code>.Data</code></dt>
<dd>numeric vector containing 5-mer mutability estimates</dd></dl>
<dt><code>source</code></dt>
<dd>character vector annotating whether the mutability was
inferred or directly measured.</dd>
<dt><code>numMutS</code></dt>
<dd>a number indicating the number of silent mutations used for 
estimating mutability</dd>
<dt><code>numMutR</code></dt>
<dd>a number indicating the number of replacement mutations used 
for estimating mutability</dd>

Slots

S4 class defining a mutability model — MutabilityModel-class

<dl>

<dt>x</dt>
<dd><code>MutabilityModel</code> object.</dd>

</dl>

<dl>
<dt><code>.Data</code></dt>
<dd>numeric vector containing 5-mer mutability estimates</dd>


<dt><code>source</code></dt>
<dd>character vector annotating whether the mutability was
inferred or directly measured.</dd>


<dt><code>numMutS</code></dt>
<dd>a number indicating the number of silent mutations used for 
estimating mutability</dd>


<dt><code>numMutR</code></dt>
<dd>a number indicating the number of replacement mutations used 
for estimating mutability</dd>


</dl>

MutabilityModel-class: S4 class defining a mutability model

Description

Usage

Arguments

Slots