Estimate single-locus allele frequencies with Dcifer

Estimates per-locus allele frequencies from an allele table (optionally with a COI table). Requires dcifer (Suggests).

Usage

dcifer_slaf_wrapper(
  allele_table,
  slaf_output,
  coi_table = NULL,
  specimen_name_col = "specimen_name",
  target_name_col = "target_name",
  target_value_col = "seq",
  tol = 1e-04,
  qstart = 0.5,
  coi_lrank = 2L
)

Arguments

allele_table: Path to allele table TSV. See Inputs.
slaf_output: Path for SLAF TSV output. See Outputs.
coi_table: Optional path to COI table TSV. See Inputs.
specimen_name_col, target_name_col, target_value_col: Column names in allele_table / coi_table.
tol, qstart: Passed to dcifer::calcAfreq().
coi_lrank: Rank of the locus used by dcifer::getCOI() when coi_table is not supplied.

Value

The SLAF tibble (also written to slaf_output).

Details

Inputs

allele_table: Allele table TSV. See vignette("input-formats", package = "PGEcore").
coi_table: Optional COI table TSV. If omitted, COI is inferred with dcifer::getCOI().

Outputs

slaf_output: Single-locus allele frequencies (default columns target_name, seq, freq, sample_total).

Running

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

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

Requires dcifer (Suggests).