Analyze Intra-Cluster Genetic Variation

This function analyzes genetic diversity within clusters by identifying variant sites and calculating mutational spectra (e.g. transition and transversion rates). It uses a DNA alignment and a vector of cluster assignments (named by sequence IDs) and returns a data frame summarizing the diversity measures for each cluster as well as for the overall population.

Usage

intra_cluster_genetic_var_analysis(clusters, dna_aln)

Arguments

clusters

A named vector of cluster assignments (cluster IDs) with names corresponding to sequence IDs.

dna_aln

A matrix representing the DNA sequence alignment, where rows are sequences (named by sequence IDs) and columns represent nucleotide positions.

Value

A data frame with one row per cluster (plus a row for the overall population) containing the number of variable sites and the rates for six mutation types. Mutation rates are rounded to three decimals.