group_from_metadata

Get a character vector of samples' groups from the input metadata file

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 

group_from_metadata function

<dl><dt>.by</dt>
<dd>Character vector. Specify a column or columns in the input metadata to group by.</dd>
<dt>.metadata</dt>
<dd>Metadata object.</dd>
<dt>.sep</dt>
<dd>Character vector. Defines a separator between groups if more than one group passed in <code>.by</code>.</dd></dl>

Arguments

immunarch:::group_from_metadata("Status", data.frame(Status = c("A", "A", "B", "B", "C")))

Developer Examples

Get a character vector of samples' groups from the input metadata file — group_from_metadata

<dl>

<dt>.by</dt>
<dd>Character vector. Specify a column or columns in the input metadata to group by.</dd>


<dt>.metadata</dt>
<dd>Metadata object.</dd>


<dt>.sep</dt>
<dd>Character vector. Defines a separator between groups if more than one group passed in <code>.by</code>.</dd>

</dl>

immunarch:::group_from_metadata("Status", data.frame(Status = c("A", "A", "B", "B", "C")))

group_from_metadata: Get a character vector of samples' groups from the input metadata file

Description

Usage

Value

Arguments

Developer Examples