compute_distance

Compute a pairwise distance matrix between sequences using stringdist.

internal

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

compute_distance function

<dl><dt>sequences</dt>
<dd>A named character vector of sequences</dd>
<dt>method</dt>
<dd>Distance method: "hamming" or "lv" (Levenshtein). Default is "hamming".</dd>
<dt>trim_3prime</dt>
<dd>Optional position to trim sequences from 3' end</dd>
<dt>quiet</dt>
<dd>Logical. Suppress messages. Default is TRUE.</dd>
<dt>return_type</dt>
<dd>One of "dist" (default) or "matrix"</dd></dl>

Arguments

Compute distance matrix — compute_distance

<dl>

<dt>sequences</dt>
<dd>A named character vector of sequences</dd>


<dt>method</dt>
<dd>Distance method: "hamming" or "lv" (Levenshtein). Default is "hamming".</dd>


<dt>trim_3prime</dt>
<dd>Optional position to trim sequences from 3' end</dd>


<dt>quiet</dt>
<dd>Logical. Suppress messages. Default is TRUE.</dd>


<dt>return_type</dt>
<dd>One of "dist" (default) or "matrix"</dd>

</dl>

compute_distance: Compute distance matrix

Description

Usage

Value

Arguments

See Also