Estimate multilocus haplotype frequencies with MultiLociBiallelicModel

Estimates multilocus haplotype frequencies from amino-acid calls and loci groups. Samples with any missing genotype are dropped (legacy behaviour; the model cannot handle missing data). Requires variantstring 1.x (Suggests).

Usage

MultiLociBiallelicModel_wrapper(
  aa_calls,
  loci_groups,
  mlaf_output,
  aa_sample_occurence_cut_off = 0
)

Arguments

aa_calls: Path to amino-acid calls TSV. See Inputs.
loci_groups: Path to loci-groups TSV. See Inputs.
mlaf_output: Output TSV path. See Outputs.
aa_sample_occurence_cut_off: Amino-acid calls must occur in more than this number of samples to be included (legacy default 0).

Value

The bound MLAF tibble (invisibly after writing mlaf_output).

Details

Inputs

aa_calls: Amino-acid calls TSV (specimen_name, gene_id, aa_position, ref_aa, aa). See vignette("input-formats", package = "PGEcore").
loci_groups: Loci-groups TSV (group_id, gene_id, aa_position).

Outputs

mlaf_output: Multilocus allele frequencies (group_id, variant, freq).

Running

MultiLociBiallelicModel_wrapper(
  aa_calls = "aa_calls.tsv",
  loci_groups = "loci_groups.tsv",
  mlaf_output = "mlaf.tsv"
)

Rscript exec/MultiLociBiallelicModel_wrapper \
  --aa_calls aa_calls.tsv \
  --loci_groups loci_groups.tsv \
  --mlaf_output mlaf.tsv

Requires variantstring (Suggests).