rduckhts_ancestry_geno: Estimate ancestry from a materialized 'read_geno' relation

In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

Estimate ancestry from a materialized 'read_geno' relation

Description

Converts each diploid, biallelic call to ALT dosage / 2. A haploid, partially missing, or multiallelic call has NULL dosage and is counted in the missing-site audit. Original sample indices identify the calls unless a 'read_bcf_samples' relation is provided for original-header sample names. That relation must give every selected sample index one distinct non-null name.

Usage

rduckhts_ancestry_geno(
  con,
  geno_table,
  reference_table,
  loadings_table,
  correction_table,
  samples_table = NULL,
  sum_to_one = TRUE,
  min_cor = 0.4,
  non_reference_only
)

Arguments

con	Connection with DuckHTS loaded.
geno_table	Materialized 'read_geno' rows with CHROM, POS, REF, ALT and calls columns. Each site must contain a call for every selected sample, including homozygous-reference calls.
reference_table, loadings_table, correction_table	Reference products.
samples_table	Optional 'read_bcf_samples' relation with sample_index and sample_name.
sum_to_one, min_cor	Quality/constraint arguments for the solver.
non_reference_only	Required declaration of the 'read_geno' setting used to create 'geno_table'. Must be 'FALSE': sparse call lists omit zero dosages and cannot be identified from the materialized relation's schema.

Value

A row per sample and group with the matching audit.

Rduckhts documentation built on Oct. 25, 2026, 1:08 a.m.