recentAlleleClusters

A wrapper function for <code>zenodoArchive</code>, download the most recent allele similarity clusters and thresholds from the zenodo archive.
The clusters and thresholds are based on <a href="https://yaarilab.github.io/IGHV_reference_book/">https://yaarilab.github.io/IGHV_reference_book/</a>
At the moment only available for human IGHV reference set.

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

recentAlleleClusters function

<dl><dt>doi</dt>
<dd>The doi for the archive to download. Default is the IGHV set.</dd>
<dt>path</dt>
<dd>The output folder for saving the archive files. Default is to a temporary directory.</dd>
<dt>get_file</dt>
<dd>Logical (FALSE by default). Do you want to return the path for the file downloaded.</dd>
<dt>quite</dt>
<dd>Logical (FALSE by default). Do you want to suppress informative messages</dd></dl>

Arguments

A wrapper function for <code>zenodoArchive</code>, download the most recent allele similarity clusters and thresholds from the zenodo archive.
The clusters and thresholds are based on <a href='https://yaarilab.github.io/IGHV_reference_book/'>https://yaarilab.github.io/IGHV_reference_book/</a>
At the moment only available for human IGHV reference set.

Retrieving allele similarity clusters Zenodo archive — recentAlleleClusters

<dl>

<dt>doi</dt>
<dd>The doi for the archive to download. Default is the IGHV set.</dd>


<dt>path</dt>
<dd>The output folder for saving the archive files. Default is to a temporary directory.</dd>


<dt>get_file</dt>
<dd>Logical (FALSE by default). Do you want to return the path for the file downloaded.</dd>


<dt>quite</dt>
<dd>Logical (FALSE by default). Do you want to suppress informative messages</dd>

</dl>

recentAlleleClusters: Retrieving allele similarity clusters Zenodo archive

Description

Usage

Value

Arguments

Examples