RegionDefinition-class

RegionDefinition

<code>RegionDefinition</code> defines a common data structure for defining the region
boundaries of an Ig sequence.

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

RegionDefinition-class function

<dl>
<dt><code>name</code></dt>
<dd>name of the RegionDefinition.</dd></dl>
<dt><code>description</code></dt>
<dd>description of the model and its source.</dd>
<dt><code>boundaries</code></dt>
<dd><code>factor</code> defining the region boundaries of the 
sequence. The levels and values of <code>boundaries</code> 
determine the number of regions.</dd>
<dt><code>seqLength</code></dt>
<dd>length of the sequence.</dd>
<dt><code>regions</code></dt>
<dd>levels of the boundaries; e.g, <code>c("cdr", "fwr")</code>.</dd>
<dt><code>labels</code></dt>
<dd>labels for the boundary and mutations combinations;
e.g., <code>c("cdr_r", "cdr_s", "fwr_r", "fwr_s")</code>.</dd>
<dt><code>citation</code></dt>
<dd>publication source.</dd>

Slots

S4 class defining a region definition — RegionDefinition-class

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


<dt><code>description</code></dt>
<dd>description of the model and its source.</dd>


<dt><code>boundaries</code></dt>
<dd><code>factor</code> defining the region boundaries of the 
sequence. The levels and values of <code>boundaries</code> 
determine the number of regions.</dd>


<dt><code>seqLength</code></dt>
<dd>length of the sequence.</dd>


<dt><code>regions</code></dt>
<dd>levels of the boundaries; e.g, <code>c("cdr", "fwr")</code>.</dd>


<dt><code>labels</code></dt>
<dd>labels for the boundary and mutations combinations;
e.g., <code>c("cdr_r", "cdr_s", "fwr_r", "fwr_s")</code>.</dd>


<dt><code>citation</code></dt>
<dd>publication source.</dd>


</dl>

S4 class defining a region definition

RegionDefinition-class: S4 class defining a region definition

Description

Arguments

Slots

See Also