Estimate IBD-based relatedness with Dcifer

Estimates pairwise relatedness from an allele table (optionally with COI, allele frequencies, and population metadata). Requires dcifer and parallel helpers (doParallel, parallelly, foreach, iterators) (Suggests).

Usage

dcifer_ibd_wrapper(
  allele_table,
  relatedness_output,
  coi_table = NULL,
  allele_freq_table = NULL,
  specimen_name_col = "specimen_name",
  target_name_col = "target_name",
  target_value_col = "seq",
  specimen_metadata = NULL,
  pop_name_col = NULL,
  rnull = 0,
  alpha = 0.05,
  use_estm = FALSE,
  threads = 1L,
  verbose = FALSE
)

Arguments

allele_table: Path to allele table TSV. See Inputs.
relatedness_output: Path for relatedness TSV. See Outputs.
coi_table: Optional path to COI table TSV. See Inputs.
allele_freq_table: Optional path to allele-frequency TSV. See Inputs.
specimen_name_col, target_name_col, target_value_col: Column names in the allele / COI / frequency tables.
specimen_metadata: Optional metadata TSV. See Inputs.
pop_name_col: Optional population column in metadata.
rnull: Relatedness null for hypothesis testing.
alpha: Significance level.
use_estm: If TRUE, use dcifer::ibdEstM() instead of dcifer::ibdPair().
threads: Number of parallel workers.
verbose: Print parallel worker output.

Value

The relatedness tibble (also written to relatedness_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.
allele_freq_table: Optional SLAF TSV (target_name, seq, freq). If omitted, frequencies are estimated from the allele table.
specimen_metadata: Optional metadata TSV for population-specific runs (with pop_name_col).

Outputs

relatedness_output: Relatedness TSV with specimen_name_a, specimen_name_b, btwn_host_rel, and optionally p_value, CI_lower, CI_upper, and/or strain_pair.

Running

dcifer_ibd_wrapper(
  allele_table = "allele_table.tsv",
  relatedness_output = "relatedness.tsv"
)

Rscript exec/dcifer_ibd_wrapper \
  --allele_table allele_table.tsv \
  --relatedness_output relatedness.tsv

Requires dcifer and parallel Suggests packages.