alleleClusterNames: Allele similarity cluster naming scheme

In piglet: Program for Inferring Immunoglobulin Allele Similarity Clusters and Genotypes

Allele similarity cluster naming scheme

Description

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

Usage

alleleClusterNames(cluster, allele.cluster.table, germ.dist, chain, segment)

Arguments

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

Value

A data.frame with the clusters renamed alleles based on the ASC scheme.

piglet documentation built on April 12, 2025, 1:27 a.m.