Run malaria.em from allele-table and output paths

Reads an allele table, builds the EM matrix, and calls run_malariaem(). Requires malaria.em (Suggests).

Usage

malariaem_wrapper(
  allele_table,
  subset_targets = FALSE,
  target_groups = NULL,
  max_size = "8",
  test_size = "min",
  freq_output = "gt_freq_summary_all.tsv",
  phase_output = "gt_phase_summary_all.tsv"
)

Arguments

allele_table

Path to allele table TSV. See Inputs.

subset_targets

Logical; subset by target_groups.

target_groups

Optional path to groups TSV. See Inputs.

max_size

COI cutoff (legacy CLI default "8").

test_size

COI size to test, or "min".

freq_output

Frequency summary path. See Outputs.

phase_output

Phase summary path. See Outputs.

Value

The object returned by run_malariaem().

Details

Inputs

• allele_table: Allele table TSV (specimen_name, target_name, seq). See vignette("input-formats", package = "PGEcore").

• target_groups: Optional groups TSV (group_id, target_name) when subset_targets = TRUE.

Outputs

• freq_output: Genotype-frequency TSV (gt_id, target_name, seq, freq, freq_se).

• phase_output: Phasing TSV (specimen_name, target_name, seq, gt_id, posterior_est, phase_id).

Running

malariaem_wrapper(
  allele_table = "allele_table.tsv",
  freq_output = "gt_freq_summary_all.tsv",
  phase_output = "gt_phase_summary_all.tsv"
)

Rscript exec/malariaem_wrapper \
  --allele_table allele_table.tsv \
  --freq_output gt_freq_summary_all.tsv \
  --phase_output gt_phase_summary_all.tsv

Requires malaria.em (Suggests).

See also

run_malariaem(), vignette("input-formats", package = "PGEcore")