Run malaria.em and write frequency and phase summaries

Runs malaria.em haplotype EM on an in-memory allele matrix and writes genotype-frequency and phasing summaries. Requires malaria.em (Suggests). For reading allele tables from disk, use malariaem_wrapper().

Usage

run_malariaem(
  matrix,
  test_size = "min",
  max_size = "8",
  subset_targets = FALSE,
  target_groups = NULL,
  freq_output = NULL,
  phase_output = NULL
)

Arguments

matrix: Allele matrix (specimens as rows, loci as columns). See Inputs.
test_size: Maximum COI to test, or "min" for the minimum allowed.
max_size: Error if inferred COI range exceeds this cutoff.
subset_targets: If TRUE, run separately for each group_id.
target_groups: Data frame with group_id and target_name. See Inputs.
freq_output: Path for genotype-frequency TSV. See Outputs.
phase_output: Path for phasing TSV. See Outputs.

Value

A list of malaria.em results (or a named list per group).

Details

Inputs

matrix: Allele matrix (specimens as rows, loci as columns; alleles space-separated within cells).
target_groups: Optional data frame with group_id and target_name when subset_targets = TRUE.

Outputs

freq_output: Genotype-frequency TSV (gt_id, target_name, seq, freq, freq_se; plus group_id when subsetting).
phase_output: Phasing TSV (specimen_name, target_name, seq, gt_id, posterior_est, phase_id; plus group_id when subsetting).

Running

run_malariaem(
  matrix = allele_matrix,
  freq_output = "gt_freq_summary_all.tsv",
  phase_output = "gt_phase_summary_all.tsv"
)

File and CLI users should call malariaem_wrapper() / Rscript exec/malariaem_wrapper ....

Requires malaria.em (Suggests).