ighvClust

This function is deprecated. Use <code>igClust</code> instead.

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

ighvClust function

<dl><dt>germline_distance</dt>
<dd>A germline set distance matrix created by <code>igDistance</code>.</dd>
<dt>family_threshold</dt>
<dd>The similarity threshold for family level (hierarchical only). Default is 75.</dd>
<dt>allele_cluster_threshold</dt>
<dd>The similarity threshold for allele cluster level (hierarchical only). Default is 95.</dd>
<dt>cluster_method</dt>
<dd>The hierarchical clustering linkage method. Default is "complete".</dd></dl>

Arguments

Allele similarity clustering (deprecated) — ighvClust

<dl>

<dt>germline_distance</dt>
<dd>A germline set distance matrix created by <code>igDistance</code>.</dd>


<dt>family_threshold</dt>
<dd>The similarity threshold for family level (hierarchical only). Default is 75.</dd>


<dt>allele_cluster_threshold</dt>
<dd>The similarity threshold for allele cluster level (hierarchical only). Default is 95.</dd>


<dt>cluster_method</dt>
<dd>The hierarchical clustering linkage method. Default is "complete".</dd>

</dl>

ighvClust: Allele similarity clustering (deprecated)

Description

Usage

Value

Arguments

See Also