Calculate Allele Frequencies from MCMC Results

Usage

calculate_allele_frequencies(
  results,
  snp_indices,
  use_map = TRUE,
  n_samples = 100,
  interval = 0.95,
  allele_sep = "|"
)

Arguments

results

A snp_slice_results object containing MCMC results

snp_indices

A vector of SNP indices to treat as a single allele

use_map

Logical, whether to use MAP estimates (TRUE) or sample from MCMC (FALSE)

n_samples

Number of MCMC samples to use if use_map = FALSE (default: 100)

interval

Numeric in (0, 1). Credible interval width when using MCMC (e.g. 0.95).

allele_sep

Separator for allele strings (default: "|")

Value

The structure depends on use_map.

MAP (use_map = TRUE)

Data frame with columns: allele (string representation of the allele, e.g. "ref|alt|ref" for 3 SNPs), frequency (proportion of total parasites with this allele; sums to 1), count (number of parasites with this allele in the MAP allocation), total_parasites (total parasites in the MAP allocation; same for every row).

MCMC (use_map = FALSE)

Data frame with columns: allele, frequency (posterior mean proportion), frequency_sd (posterior SD of proportion across samples), frequency_lower and frequency_upper (credible interval, e.g. 2.5\

Calculates allele frequencies for a collection of SNPs treated as a single allele. The function takes SNP indices and calculates the frequency of each possible allele combination across all individuals based on their strain allocations. With use_map = FALSE, counts are summarized as per-sample means rather than sums, so mean_count and mean_total_parasites are interpretable regardless of n_samples. Frequency uncertainty (frequency_sd, frequency_lower, frequency_upper) is computed from the distribution of allele frequencies across MCMC samples. # Load example results result <- load_example_results()# Calculate allele frequencies for SNPs 1, 5, and 10 (MAP) allele_freqs <- calculate_allele_frequencies(result, c(1, 5, 10)) print(allele_freqs)# With MCMC: posterior mean, SD, credible interval, and per-sample mean count if (!is.null(result$mcmc_samples)) allele_freqs_mcmc <- calculate_allele_frequencies(result, c(1, 5, 10), use_map = FALSE, n_samples = 50) print(allele_freqs_mcmc)