ScoperClones-class

ScoperClones

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ScoperClones-method

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<code>ScoperClones</code> stores output from identicalClones, hierarchicalClones and
spectralClones functions.

Provides a computational framework for identification of B cell clones from
Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. Three main
functions are included (identicalClones, hierarchicalClones, and spectralClones)
that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins)
which share the same V gene, J gene and junction length.
Nouri N and Kleinstein SH (2018) <doi: 10.1093/bioinformatics/bty235>.
Nouri N and Kleinstein SH (2019) <doi: 10.1101/788620>.
Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>.

Susanna Marquez

scoper

Spectral Clustering-Based Method for Identifying B Cell Clones

Nima Nouri

Edel Aron

Gisela Gabernet

Jason Vander Heiden

Steven Kleinstein

ScoperClones-class function

<dl><dt>x</dt>
<dd>ScoperClones object</dd>
<dt>object</dt>
<dd>ScoperClones object</dd>
<dt>y</dt>
<dd>ignored.</dd>
<dt>...</dt>
<dd>arguments to pass to plotCloneSummary.</dd></dl>

Arguments

<dl>
<dt><code>db</code></dt>
<dd><code>data.frame</code> of repertoire data including with clonal identifiers in 
the column specified during processing.</dd></dl>
<dt><code>vjl_groups</code></dt>
<dd><code>data.frame</code> of clonal summary, including sequence count, V gene, 
J gene, junction length, and clone counts.</dd>
<dt><code>inter_intra</code></dt>
<dd><code>data.frame</code> containing minimum inter (between) and maximum intra 
(within) clonal distances.</dd>
<dt><code>eff_threshold</code></dt>
<dd>effective cut-off separating the inter (between) and intra (within) clonal 
distances.</dd>

Slots

S4 class containing clonal assignments and summary data — ScoperClones-class

<dl>

<dt>x</dt>
<dd>ScoperClones object</dd>


<dt>object</dt>
<dd>ScoperClones object</dd>


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


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

</dl>

<dl>
<dt><code>db</code></dt>
<dd><code>data.frame</code> of repertoire data including with clonal identifiers in 
the column specified during processing.</dd>


<dt><code>vjl_groups</code></dt>
<dd><code>data.frame</code> of clonal summary, including sequence count, V gene, 
J gene, junction length, and clone counts.</dd>


<dt><code>inter_intra</code></dt>
<dd><code>data.frame</code> containing minimum inter (between) and maximum intra 
(within) clonal distances.</dd>


<dt><code>eff_threshold</code></dt>
<dd>effective cut-off separating the inter (between) and intra (within) clonal 
distances.</dd>


</dl>

ScoperClones-class: S4 class containing clonal assignments and summary data

Description

Usage

Arguments

Slots

See Also