Calculate allele frequencies for multiple target sets — calculate_allele_frequencies_by

For each target set, computes allele frequencies from MCMC/MAP results and returns a list of frequency tables (one per set). Each set is a vector of target indices or target names.

Usage

calculate_allele_frequencies_by_sets(
  results,
  target_sets,
  use_map = TRUE,
  n_samples = 100,
  interval = 0.95,
  allele_sep = "|"
)

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.
use_map: Logical; use MAP estimates (TRUE) or sample from MCMC (FALSE).
n_samples: Number of MCMC samples to use if use_map = FALSE (default: 100).
interval: Credible interval width when use_map = FALSE (e.g. 0.95).
allele_sep: Separator for allele strings (default: "|").

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: with MAP, columns allele, frequency, count, total_parasites; with MCMC, 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 0.70793037   366             517
#> 2 ref|alt 0.15667311    81             517
#> 3 alt|ref 0.11025145    57             517
#> 1 alt|alt 0.02514507    13             517