distance_to_graph

Converts a distance matrix to a weighted igraph object using a log transform
that spreads small distances and produces weights in [0,1].

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

distance_to_graph function

<dl><dt>distance_matrix</dt>
<dd>A distance matrix or dist object</dd></dl>

Arguments

Convert distance matrix to weighted graph — distance_to_graph

<dl>

<dt>distance_matrix</dt>
<dd>A distance matrix or dist object</dd>

</dl>

distance_to_graph: Convert distance matrix to weighted graph

Description

Usage

Value

Arguments

Details

See Also

Examples