piglet (version 1.0.7)

ighvClust: 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"
)

Value

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

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".