ighvClust: Allele similarity clustering

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

Allele similarity clustering

Description

Cluster the distance matrix from ighvDistance to create the allele clusters based on two thresholds: 75% similarity which represents the family clustering and 95% similarity between alleles which represents the allele clusters

Usage

ighvClust(
  germline_distance,
  family_threshold = 75,
  allele_cluster_threshold = 95,
  cluster_method = "complete"
)

Arguments

germline_distance	A germline set distance matrix created by ighvDistance.
family_threshold	The similarity threshold for the family level. Default is 75.
allele_cluster_threshold	The similarity threshold for the allele cluster level. Default is 95.
cluster_method	The hierarchical clustering method to use. Default is "complete".

Value

A names list that includes the data.frame of the alleles clusters, the thresholds parameters and the hierarchical clustering of the germline set.

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