Compute intra-cluster SNP-distance summaries

Returns the mean, median and maximum pairwise SNP distance within a single cluster, taken from the upper triangle of the cluster's own submatrix (excluding the diagonal). Inter-cluster and inter-isolate distances are computed separately, over all clusters at once, by cluster_inter_distances().

Usage

cluster_pairwise_distances(cluster_seqs, snp_dist)

Arguments

cluster_seqs

Vector of sequence IDs in the cluster.

snp_dist

Matrix of SNP distances between isolates.

Value

A named numeric vector with mean_genetic_distance, median_genetic_distance and max_genetic_distance.