ClonalAnalysis-class

ClonalAnalysis

<code>ClonalAnalysis</code> contains output from the <a rd-options="" href="/link/analyzeClones?package=scoper&version=0.1.0" data-mini-rdoc="scoper::analyzeClones">analyzeClones</a> function.
It includes infromation to interpret clonal assignment performance.

Provides a computational framework for unsupervised identification B cell clones
from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets. This method
is based on spectral clustering of the junction sequences of B cell receptors (BCRs,
also referred to as Immunoglobulins, (Igs)) that share the same V gene, J gene and junction length.

Nima Nouri

scoper

Spectral Clustering-Based Method for Identifying B Cell Clones

Jason Vander Heiden

Steven Kleinstein

ClonalAnalysis-class function

<dl class="dl-horizontal">
<dt><code>threshold</code></dt><dd>cut-off separating the inter (within) and intra (between)
clonal distances.</dd></dl><dt><code>inter_intra</code></dt><dd>data.frame containing all inter and intra clonal distances.</dd><dt><code>plot_inter_intra</code></dt><dd>density plot of inter versus intra clonal distances. The threshold is
shown with a horizental dashed-line.</dd><dt><code>neighborhoods</code></dt><dd>a numeric vector containing scale parameters used in spectral
clustering process.</dd><dt><code>plot_neighborhoods</code></dt><dd>histogram of neighborhoods. The threshold is shown with a vertical
dashed-line.</dd>

Slots

<code>ClonalAnalysis</code> contains output from the <a rd-options='' href='analyzeClones'>analyzeClones</a> function.
It includes infromation to interpret clonal assignment performance.

ClonalAnalysis-class: Output of the analyzeClones function

Description

Arguments

Slots

See Also