Estimate single-locus allele frequencies with the Incomplete Data Model

Estimates single-locus allele frequencies with the Incomplete Data Model (or original model). Provide exactly one of allele_table or aa_calls. Vendored MLE code is from Hashemi & Schneider (2024). Requires Rmpfr and openxlsx (Suggests).

Usage

IDM_wrapper(
  allele_table = "",
  aa_calls = "",
  slaf_output,
  model = "IDM",
  lambda_initial = 1,
  eps_initial = 0.1
)

Arguments

allele_table: Path to allele table TSV, or "" / NULL if using amino-acid calls. See Inputs.
aa_calls: Path to amino-acid calls TSV, or "" / NULL if using an allele table. See Inputs.
slaf_output: Output TSV path. See Outputs.
model: "IDM" (incomplete-data model), "OM" (original model), or "IDM_OM" (IDM, falling back to the OM at any locus the IDM leaves unsolved), "OM_CC" (OM with a continuity correction on lineage prevalence), or "IDM_OM_CC" (IDM, falling back to "OM_CC").
lambda_initial: Initial lambda for the numerical iteration.
eps_initial: Initial epsilon for the numerical iteration.

Value

The SLAF tibble (invisibly after writing slaf_output).

Details

Inputs

allele_table: Allele table TSV, or "" / NULL if using aa_calls. See vignette("input-formats", package = "PGEcore").
aa_calls: Amino-acid calls TSV, or "" / NULL if using allele_table.

Outputs

slaf_output: Single-locus allele frequencies. Allele-table input is written as target_name, seq, freq; AA-call input as variant, freq.

Running

IDM_wrapper(
  allele_table = "allele_table.tsv",
  slaf_output = "slaf.tsv"
)

Rscript exec/IDM_wrapper \
  --allele_table allele_table.tsv \
  --slaf_output slaf.tsv

Requires Rmpfr and openxlsx (Suggests).