GermlineCluster is an S3 class that stores the output of
inferAlleleClusters. It contains the allele cluster table,
clustering objects, and threshold parameters used for inference.
new_germline_cluster(
germlineSet,
alleleClusterSet,
alleleClusterTable,
threshold,
hclustAlleleCluster = NULL,
clusteringMethod = "hierarchical",
communityObject = NULL,
graphObject = NULL,
distanceMatrix = NULL,
silhouetteScore = NA_real_,
resolutionParameter = NA_real_,
locus = "IGHV"
)An object of class "GermlineCluster".
The original germline set provided.
The renamed germline set with allele clusters.
The allele cluster table.
The threshold used for family and allele clusters.
A hierarchical clustering object for the germline set,
or NULL.
The clustering method used, either "hierarchical"
or "leiden".
A community detection object for Leiden clustering, or NULL.
An igraph graph object for Leiden clustering, or NULL.
The distance matrix used for clustering, or NULL.
The silhouette score for community detection.
The resolution parameter used for Leiden clustering.
The locus identifier, for example "IGHV", "IGHD", "IGHJ".
inferAlleleClusters
GermlineCluster