DiversityCurve

DiversityCurve-class

print,DiversityCurve-method


<code>DiversityCurve</code> defines diversity ($D$) scores over multiple diversity 
orders ($Q$).


Provides immunoglobulin (Ig) sequence lineage reconstruction,
diversity profiling, and amino acid property analysis. Also provides
core functionality for other tools in the Change-O suite.

Jason Vander Heiden

alakazam

Immunoglobulin Clonal Lineage and Diversity Analysis

DiversityCurve-class function

 <dl>
<dt><code>data</code></dt><dd>data.frame defining the diversity curve with the following columns:
<ul>
<li>  <code>GROUP</code>:    group label.
  </li>
<li>  <code>Q</code>:        diversity order.
  </li>
<li>  <code>D</code>:        mean diversity index over all bootstrap 
                          realizations.
  </li>
<li>  <code>D_SD</code>:     standard deviation of the diversity index 
                          over all bootstrap realizations.
  </li>
<li>  <code>D_LOWER</code>:  diversity lower confidence inverval bound.
  </li>
<li>  <code>D_UPPER</code>:  diversity upper confidence interval bound.
  </li>
<li>  <code>E</code>:        evenness index calculated as <code>D</code> 
                          divided by <code>D</code> at <code>Q=0</code>.
  </li>
<li>  <code>E_LOWER</code>:  evenness lower confidence inverval bound.
  </li>
<li>  <code>E_UPPER</code>:  eveness upper confidence interval bound.
</li>
</ul>
</dd> <dt><code>groups</code></dt><dd>character vector of groups retained in the diversity calculation.</dd> <dt><code>n</code></dt><dd>numeric vector indication the number of sequences sampled from each group.</dd> <dt><code>nboot</code></dt><dd>number of bootstrap realizations performed.</dd> <dt><code>ci</code></dt><dd>confidence interval defining the upper and lower bounds 
(a value between 0 and 1).</dd> </dl>

DiversityCurve-class: S4 class defining diversity curve

Description

Usage

Arguments

Slots