Calculate allele frequencies for multiple target sets — calculate_allele_frequencies_by

For each target set, computes allele frequencies and returns a list of frequency tables (one per set). Each set is a vector of target indices or target names. The estimator is chosen by the estimate argument passed through ... to calculate_allele_frequencies.

Usage

calculate_allele_frequencies_by_sets(results, target_sets, ...)

Arguments

results: A snp_slice_results object containing MCMC results.
target_sets: List of vectors; each element is target indices (integer) or target names (character) defining one set. If the list is named, those names are used for the returned list.
...: Arguments passed on to calculate_allele_frequencies.

Value

A named list of data frames, one per target set. List names come from names(target_sets) or "set_1", "set_2", etc. Each data frame has the same structure as the return value of calculate_allele_frequencies: for a point estimate ("final_sample" or "map"), columns allele, frequency, count, total_parasites; for "posterior", columns allele, frequency, frequency_sd, frequency_lower, frequency_upper, mean_count, n_samples, and attribute mean_total_parasites. See that function's help for the meaning of each column.

Examples

result <- load_example_results()
target_sets <- list(locus_a = c(1, 5), locus_b = c(10))
freqs <- calculate_allele_frequencies_by_sets(result, target_sets)
print(freqs$locus_a)
#>    allele  frequency count total_parasites
#> 4 ref|ref 0.70857143   372             525
#> 2 ref|alt 0.15238095    80             525
#> 3 alt|ref 0.12761905    67             525
#> 1 alt|alt 0.01142857     6             525