allele_diff_indices

Calculate differences between characters in columns of germs and return their indices as an int vector.

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_diff_indices function

<dl><dt>germs</dt>
<dd>A vector of strings representing germ sequences.</dd>
<dt>X</dt>
<dd>The threshold index from which to return differences as indices.</dd>
<dt>non_mismatch_chars_nullable</dt>
<dd>A set of characters that are ignored when comparing sequences (default: 'N', '.', '-').</dd></dl>

Arguments

Calculate differences between characters in columns of germs and return their indices as an int vector. — allele_diff_indices

<dl>

<dt>germs</dt>
<dd>A vector of strings representing germ sequences.</dd>


<dt>X</dt>
<dd>The threshold index from which to return differences as indices.</dd>


<dt>non_mismatch_chars_nullable</dt>
<dd>A set of characters that are ignored when comparing sequences (default: 'N', '.', '-').</dd>

</dl>

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allele_diff_indices: Calculate differences between characters in columns of germs and return their indices as an int vector.

Description

Usage

Value

Arguments

Examples