MRCATest-class

MRCATest

print,MRCATest-method

MRCATest-method

plot,MRCATest,missing-method

<code>MRCATest</code> defines the significance of enrichment for annotations appearing at
the MRCA of the tree.

Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.

Jason Vander Heiden

alakazam

Immunoglobulin Clonal Lineage and Diversity Analysis

Susanna Marquez

Namita Gupta

Nima Nouri

Ruoyi Jiang

Julian Zhou

Kenneth Hoehn

Daniel Gadala-Maria

Edel Aron

Steven Kleinstein

MRCATest-class function

<dl><dt>x</dt>
<dd>MRCATest object.</dd>
<dt>y</dt>
<dd>ignored.</dd>
<dt>...</dt>
<dd>arguments to pass to plotMRCATest.</dd></dl>

Arguments

<dl>
<dt><code>tests</code></dt>
<dd>data.frame describing the significance test results with columns:<ul>
<li><code>annotation</code>: annotation value.</li>
<li><code>count</code>: observed count of MRCA positions 
 with the given annotation.</li>
<li><code>expected</code>: expected mean count of MRCA occurance
 for the annotation.</li>
<li><code>pvalue</code>: one-sided p-value for the hypothesis that 
 the observed annotation abundance is greater 
 than expected.</li>
</ul></dd></dl>
<dt><code>permutations</code></dt>
<dd>data.frame containing the raw permutation test data with columns:<ul>
<li><code>annotation</code>: annotation value.</li>
<li><code>count</code>: count of MRCA positions with the 
 given annotation.</li>
<li><code>iter</code>: numerical index define which 
 permutation realization each 
 observation corresponds to.</li>
</ul></dd>
<dt><code>nperm</code></dt>
<dd>number of permutation realizations.</dd>

Slots

S4 class defining edge significance — MRCATest-class

<dl>

<dt>x</dt>
<dd>MRCATest object.</dd>


<dt>y</dt>
<dd>ignored.</dd>


<dt>...</dt>
<dd>arguments to pass to plotMRCATest.</dd>

</dl>

<dl>
<dt><code>tests</code></dt>
<dd>data.frame describing the significance test results with columns:<ul>
<li><code>annotation</code>: annotation value.</li>
<li><code>count</code>: observed count of MRCA positions 
 with the given annotation.</li>
<li><code>expected</code>: expected mean count of MRCA occurance
 for the annotation.</li>
<li><code>pvalue</code>: one-sided p-value for the hypothesis that 
 the observed annotation abundance is greater 
 than expected.</li>
</ul></dd>


<dt><code>permutations</code></dt>
<dd>data.frame containing the raw permutation test data with columns:<ul>
<li><code>annotation</code>: annotation value.</li>
<li><code>count</code>: count of MRCA positions with the 
 given annotation.</li>
<li><code>iter</code>: numerical index define which 
 permutation realization each 
 observation corresponds to.</li>
</ul></dd>


<dt><code>nperm</code></dt>
<dd>number of permutation realizations.</dd>


</dl>

MRCATest-class: S4 class defining edge significance

Description

Usage

Arguments

Slots