rduckhts_ancestry_panel: Create a deterministic ancestry site panel for BAM/CRAM...
In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

rduckhts_ancestry_panel

R Documentation

Create a deterministic ancestry site panel for BAM/CRAM counts

Description

Sites are biallelic unambiguous SNVs present in every reference group and every PC loading. Positions are positive one-based whole numbers and all group alleles must be present. With 'candidate_table', only matching candidate loci and alleles are retained. Otherwise one site is selected per chromosome/spaced genomic window. Results are sorted by chromosome and position and assigned dense zero-based panel ordinals. Keep the returned panel SHA-256 and the reference release with the materialized panel as its versioned identity.

Usage

rduckhts_ancestry_panel(
  con,
  reference_table,
  loadings_table,
  table_name,
  assembly,
  candidate_table = NULL,
  spacing_bp = 5000,
  max_sites = 17000,
  overwrite = FALSE
)

Arguments

`con`	A connection with DuckHTS loaded.
`reference_table`, `loadings_table`	Reference products on the connection.
`table_name`	Destination committed panel relation, visible to the BAM/CRAM panel preparation path.
`assembly`	Reference genome assembly label.
`candidate_table`	Optional site panel, e.g. a Somalier panel with region, position, allele_a and allele_b.
`spacing_bp`	Genomic window width for deterministic spacing.
`max_sites`	Maximum number of selected sites. When more sites are eligible, each contig keeps at least one site (the largest contigs, when 'max_sites' is below the contig count), the rest are shared by largest remainders in proportion to each contig's eligible sites minus that one (its remaining capacity, so no contig is offered more than it has), and each contig's sites are spread evenly along it.
`overwrite`	Replace an existing destination.