Cluster the distance matrix to create allele clusters. Supports both hierarchical clustering (default) and Leiden community detection.
igClust(
germline_distance,
method = c("hierarchical", "leiden"),
family_threshold = 75,
allele_cluster_threshold = 95,
cluster_method = "complete",
resolution = NULL,
target_clusters = NULL,
optimize_silhouette = TRUE,
ncores = 1,
quiet = FALSE
)A named list that includes:
alleleClusterTable: data.frame of allele clusters
threshold: list of threshold parameters
hclustAlleleCluster: hierarchical clustering object (hierarchical method)
communityObject: community detection result (Leiden method)
graphObject: igraph object (Leiden method)
silhouetteScore: silhouette score (Leiden method)
resolutionParameter: resolution used (Leiden method)
A germline set distance matrix created by igDistance.
Clustering method. One of "hierarchical" (default) or "leiden".
The similarity threshold for family level (hierarchical only). Default is 75.
The similarity threshold for allele cluster level (hierarchical only). Default is 95.
The hierarchical clustering linkage method. Default is "complete".
Resolution parameter for Leiden clustering. If NULL, will be optimized.
Target number of clusters for Leiden optimization. Default is NULL.
Logical. Optimize resolution using silhouette score (Leiden only). Default is TRUE.
Number of cores for parallel processing (Leiden only). Default is 1.
Logical. Suppress messages. Default is FALSE.
igDistance, inferAlleleClusters