GermlineCluster-class

GermlineCluster

plot,GermlineCluster,missing-method

plot,GermlineCluster,missing,

numeric

<code>GermlineCluster</code> contains output from inferAlleleClusters function.
It includes the allele cluster table, the germline set hierarchical clustering,
and the threshold parameters.

Improves genotype inference and downstream Adaptive Immune Receptor Repertoire Sequence data analysis. Inference of allele similarity clusters, an alternative naming scheme and genotype inference for immunoglobulin heavy chain repertoires.
The main tools are allele similarity clusters, and allele based genotype. The first tool is designed to reduce the ambiguity within the immunoglobulin heavy chain V alleles. The ambiguity is caused by duplicated or similar alleles which are shared among different genes.
The second tool is an allele based genotype, that determined the presence of an allele based on a threshold derived from a naive population. See Peres et al. (2023) <doi:10.1093/nar/gkad603>.

Ayelet Peres

piglet

Program for Inferring Immunoglobulin Allele Similarity Clusters
and Genotypes

William Lees

Gur Yaari

GermlineCluster-class function

<dl><dt>x</dt>
<dd>GermlineCluster object</dd>
<dt>y</dt>
<dd>not in use. missing.</dd>
<dt>cex</dt>
<dd>Controls the size of the allele label. Default is 1.</dd>
<dt>seed</dt>
<dd>Set a seed number for drawing the dendrogram. Default 9999.</dd></dl>

Arguments

<ul>
<li><code>plot(x = GermlineCluster, y = missing)</code>: Plot the dendrogram for the allele clusters.</li>
</ul>

Methods (by generic)

<dl>
<dt><code>germlineSet</code></dt>
<dd>the original germline set provided</dd></dl>
<dt><code>alleleClusterSet</code></dt>
<dd>the renamed germline set with the allele clusters</dd>
<dt><code>alleleClusterTable</code></dt>
<dd>the allele cluster table</dd>
<dt><code>hclustAlleleCluster</code></dt>
<dd>the hierarchical clustering object of the germline set.</dd>
<dt><code>threshold</code></dt>
<dd>the threshold used for the family and the allele clusters.</dd>

Slots

Output of inferAlleleClusters — GermlineCluster-class

<dl>

<dt>x</dt>
<dd>GermlineCluster object</dd>


<dt>y</dt>
<dd>not in use. missing.</dd>


<dt>cex</dt>
<dd>Controls the size of the allele label. Default is 1.</dd>


<dt>seed</dt>
<dd>Set a seed number for drawing the dendrogram. Default 9999.</dd>

</dl>

<dl>
<dt><code>germlineSet</code></dt>
<dd>the original germline set provided</dd>


<dt><code>alleleClusterSet</code></dt>
<dd>the renamed germline set with the allele clusters</dd>


<dt><code>alleleClusterTable</code></dt>
<dd>the allele cluster table</dd>


<dt><code>hclustAlleleCluster</code></dt>
<dd>the hierarchical clustering object of the germline set.</dd>


<dt><code>threshold</code></dt>
<dd>the threshold used for the family and the allele clusters.</dd>


</dl>

GermlineCluster-class: Output of inferAlleleClusters

Description

Usage

Arguments

Methods (by generic)

Slots

See Also