RegionDefinition

RegionDefinition-class


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


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

RegionDefinition-class function

 <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>

RegionDefinition-class: S4 class defining a region definition

Description

Arguments

Slots

See Also