TargetingMatrix-class

TargetingMatrix

<code>TargetingMatrix</code> defines a data structure for just the targeting matrix 
(as opposed to the entire <code>TargetingModel</code>)

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

TargetingMatrix-class function

<dl>
<dt><code>.Data</code></dt>
<dd>matrix.</dd></dl>
<dt><code>numMutS</code></dt>
<dd>number indicating the number of silent mutations used for 
estimating mutability.</dd>
<dt><code>numMutR</code></dt>
<dd>number indicating the number of replacement mutations used 
for estimating mutability.</dd>

Slots

S4 class defining a targeting matrix — TargetingMatrix-class

<dl>
<dt><code>.Data</code></dt>
<dd>matrix.</dd>


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


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


</dl>

S4 class defining a targeting matrix

TargetingMatrix-class: S4 class defining a targeting matrix

Description

Arguments

Slots