DiversityTest

DiversityTest-class

print,DiversityTest-method


<code>DiversityTest</code> defines the signifance of diversity ($D$) differences at a 
fixed diversity order ($q$).


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

DiversityTest-class function

 <dl>
<dt><code>tests</code></dt><dd>data.frame describing the significance test results with columns:
<ul>
<li>  <code>test</code>:          string listing the two groups tested.
  </li>
<li>  <code>pvalue</code>:        p-value for the test.
  </li>
<li>  <code>delta_mean</code>:    mean of the $D$ bootstrap delta 
                               distribution for the test.
  </li>
<li>  <code>delta_sd</code>:      standard deviation of the $D$ 
                               bootstrap delta distribution for the test.
</li>
</ul>
</dd> <dt><code>summary</code></dt><dd>data.frame containing summary statistics for the diversity index 
bootstrap distributions, at the given value of $q$, with columns:
<ul>
<li>  <code>group</code>:   the name of the group.
  </li>
<li>  <code>mean</code>:    mean of the $D$ bootstrap distribution.
  </li>
<li>  <code>sd</code>:      standard deviation of the $D$ bootstrap 
                         distribution.
</li>
</ul>
</dd> <dt><code>groups</code></dt><dd>character vector of groups retained in diversity calculation.</dd> <dt><code>q</code></dt><dd>diversity order tested ($q$).</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.</dd> </dl>

DiversityTest-class: S4 class defining diversity significance

Description

Usage

Arguments

Slots