Compute genetic distances by cluster — compute_genetic_distances_by_cluster • hospitraceR

Summarize intra-cluster SNP distances (mean/median/max) for every multi-patient cluster in an isolate lookup, via cluster_pairwise_distances().

Usage

compute_genetic_distances_by_cluster(isolate_lookup, snp_dist)

Arguments

isolate_lookup: An isolate lookup table from get_isolate_lookup().
snp_dist: Matrix of SNP distances between isolates.

Value

Data frame with mean_genetic_distance, median_genetic_distance, max_genetic_distance and cluster, one row per cluster.