alleleClusterNames

For a given cluster the function collapse similar sequences and renames the sequences based on the ASC name scheme

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

alleleClusterNames function

<dl><dt>cluster</dt>
<dd>A vector with the cluster identifier - the family and allele cluster number.</dd>
<dt>allele.cluster.table</dt>
<dd>A data.frame with the list of all germline sequences and their clusters.</dd>
<dt>germ.dist</dt>
<dd>A matrix with the germline distance between the germline set sequences.</dd>
<dt>chain</dt>
<dd>A character with the chain identifier: IGH/IGL/IGK/TRB/TRA... (Currently only IGH is supported)</dd>
<dt>segment</dt>
<dd>A character with the segment identifier: IGHV/IGHD/IGHJ.... (Currently only IGHV is supported)</dd></dl>

Arguments

Allele similarity cluster naming scheme — alleleClusterNames

<dl>

<dt>cluster</dt>
<dd>A vector with the cluster identifier - the family and allele cluster number.</dd>


<dt>allele.cluster.table</dt>
<dd>A data.frame with the list of all germline sequences and their clusters.</dd>


<dt>germ.dist</dt>
<dd>A matrix with the germline distance between the germline set sequences.</dd>


<dt>chain</dt>
<dd>A character with the chain identifier: IGH/IGL/IGK/TRB/TRA... (Currently only IGH is supported)</dd>


<dt>segment</dt>
<dd>A character with the segment identifier: IGHV/IGHD/IGHJ.... (Currently only IGHV is supported)</dd>

</dl>

alleleClusterNames: Allele similarity cluster naming scheme

Description

Usage

Value

Arguments