allele_threshold_table

<p>A <code>data.table</code> of the allele thresholds table. The V alleles are based on the
<code>HVGERM</code> and <code>hv_functionality</code> germline reference set. The D, and the J are based on
the AIRR-C reference set (https://zenodo.org/records/10489725). The table contains these columns: allele - the IUIS allele name,
asc_allele - the allele name based on allele similarity clusters (only for V), threshold = the genotype threshold for the alleles.</p>

table

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

allele_threshold_table function

<p>An object of class <code>data.table</code> (inherits from <code>data.frame</code>) with 262 rows and 4 columns.</p>

allele_threshold_table: Allele thresholds table

Description

Usage

Arguments

Format

References