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
)

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.

Value¶

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