Estimate COI with coiaf from SNP-call and output paths

Reads SNP calls (and optional PLMAF), runs run_coiaf(), and writes COI estimates. Requires coiaf (Suggests).

Usage

coiaf_wrapper(snp_calls, output, plmaf = NULL, seq_error = 0.01, max_coi = 25)

Arguments

snp_calls

Path to SNP-calls TSV. See Inputs.

output

Output TSV path. See Outputs.

plmaf

Optional path to PLMAF TSV. See Inputs.

seq_error

Sequencing error rate (default: 0.01).

max_coi

Maximum COI to consider (default: 25).

Value

The result tibble (also written to output).

Details

Inputs

• snp_calls: Path to SNP-calls TSV. See vignette("input-formats", package = "PGEcore").

• plmaf: Optional path to PLMAF TSV (snp_name, seq_base, plmaf).

Outputs

• output: TSV with specimen_name, coi_freq, and coi_variant.

Running

coiaf_wrapper(
  snp_calls = "snp_calls.tsv",
  output = "coi_estimates.tsv"
)

Rscript exec/coiaf_wrapper \
  --snp_calls snp_calls.tsv \
  --output coi_estimates.tsv

Requires coiaf (Suggests).

See also

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