rduckhts_somalier_relatedness: Compare Somalier-Derived Sample Sketches

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

Compare Somalier-Derived Sample Sketches

Description

Compute the named relatedness and concordance statistics for either every distinct pair in one sketch relation or the ordered pairs in 'pairs_table'. The sketch relation must contain one non-NULL 'sketch' struct per sample. Selected pairs are an ordinary relation with 'sample_a' and 'sample_b' columns. Missing or duplicate sample and pair identities error instead of silently dropping or multiplying requested comparisons. The native kernel checks assembly, ordered-panel digest, classification settings, mask shape, and mask contents. For all pairs it checks the contents of each sketch once and then compares the checked sketches; for selected pairs it checks both sketches of each comparison. No SQL row-order guarantee is implied.

Usage

rduckhts_somalier_relatedness(
  con,
  sketches_table = NULL,
  sketches_parquet = NULL,
  pairs_table = NULL,
  table_name = NULL,
  max_sites = 1e+06,
  max_pairs = 5e+07,
  overwrite = FALSE
)

Arguments

con	A DuckDB connection with DuckHTS loaded.
sketches_table	Name of a prepared sketch table or view.
sketches_parquet	Path to ordinary Parquet-persisted sketches instead of 'sketches_table'.
pairs_table	Optional name of an ordered-pair table or view; 'NULL' requests all distinct unordered sample pairs.
table_name	Optional output table. 'NULL' returns a data frame, which should be used only for a result small enough to fit in R memory.
max_sites	Positive per-pair panel capacity, at most 100,000,000.
max_pairs	Positive cap on the number of pairs when 'pairs_table' is 'NULL'. A sketch relation of N samples has N(N-1)/2 pairs; more pairs than 'max_pairs' is an error before any pair is compared.
overwrite	Whether an existing output table may be replaced.

Value

A data frame if 'table_name' is 'NULL'; otherwise invisible 'TRUE'.

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