Get the N most abundant clonotypes

A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell
T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and
visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq)
and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods,
such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes
and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor
databases and clonotype tracking in vaccination and cancer studies. A successor to our
previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.

Vadim I. Nazarov

immunarch

Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

Vasily O. Tsvetkov

Siarhei Fiadziushchanka

Eugene Rumynskiy

Aleksandr A. Popov

Ivan Balashov

Maria Samokhina

Anna Lorenc

Daniel J. Moore

Victor Greiff

ImmunoMind 

top function

<dl><dt>.data</dt>
<dd>The data to be processed. Can be <a href="/link/data.frame?package=immunarch&version=0.9.1" data-mini-rdoc="immunarch::data.frame">data.frame</a>,
data.table, or a list of these objects.
Every object must have columns in the immunarch compatible format.
immunarch_data_format
Competent users may provide advanced data representations:
DBI database connections, Apache Spark DataFrame from copy_to or a list
of these objects. They are supported with the same limitations as basic objects.
Note: each connection must represent a separate repertoire.</dd>
<dt>.n</dt>
<dd>Numeric. Number of the most abundant clonotypes to return.</dd></dl>

Arguments

Get the N most abundant clonotypes — top

<dl>

<dt>.data</dt>
<dd>The data to be processed. Can be <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>,
data.table, or a list of these objects.
Every object must have columns in the immunarch compatible format.
immunarch_data_format
Competent users may provide advanced data representations:
DBI database connections, Apache Spark DataFrame from copy_to or a list
of these objects. They are supported with the same limitations as basic objects.
Note: each connection must represent a separate repertoire.</dd>


<dt>.n</dt>
<dd>Numeric. Number of the most abundant clonotypes to return.</dd>

</dl>

Get the N most abundant clonotypes

top: Get the N most abundant clonotypes

Description

Usage

Value

Arguments

Examples