rduckhts_somalier_charr: Estimate Per-Sample Contamination with CHARR

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

Estimate Per-Sample Contamination with CHARR

Description

Apply the Somalier-derived CHARR estimator to measured A/B/other count evidence aligned to an ordered panel and population-B allele frequencies. ‘frequency_table' contains the panel’s six identity columns plus 'population_b_af'; it must cover every panel site exactly once. Evidence and frequency identities, coordinates, and A/B orientation are checked against the panel before their digests are derived. A result with no usable homozygous-like evidence has status 'no_evidence' and a NULL estimate.

Usage

rduckhts_somalier_charr(
  con,
  evidence_table = NULL,
  evidence_parquet = NULL,
  panel_table = NULL,
  panel_parquet = NULL,
  frequency_table = NULL,
  frequency_parquet = NULL,
  table_name = NULL,
  sample_ids = NULL,
  min_depth = 15,
  max_depth = 1e+06,
  hom_minor_rate = 0.12,
  hom_tail_alpha = 0.002,
  max_threshold_work = 1.6e+07,
  max_sites = 1e+06,
  overwrite = FALSE
)

Arguments

con	A DuckDB connection with DuckHTS loaded.
evidence_table	Name of an ordinary evidence table or view.
evidence_parquet	Path to an evidence Parquet file, instead of 'evidence_table'.
panel_table	Name of the required ordered panel table or view. Panel assembly and region values are each limited to 1,024 bytes.
panel_parquet	Path to the required ordered panel Parquet file, instead of 'panel_table'.
frequency_table	Name of the required population-frequency table or view.
frequency_parquet	Path to the required population-frequency Parquet file, instead of 'frequency_table'.
table_name	Optional output table. 'NULL' returns a data frame.
sample_ids	Optional nonempty vector of distinct sample IDs to retain.
min_depth	Minimum measured A+B depth for CHARR homozygous-like eligibility.
max_depth	Maximum supported A+B depth for the binomial eligibility test, at most 1,000,000.
hom_minor_rate	Expected minor-read rate used to recognize homozygous-like anchors.
hom_tail_alpha	Binomial upper-tail threshold for homozygous-like eligibility.
max_threshold_work	Positive cumulative limit on exact binomial certification steps, at most 100,000,000. Distinct observed depths are certified once per call and shared across samples.
max_sites	Positive per-sample panel capacity, at most 100,000,000.
overwrite	Whether an existing output table may be replaced.

Details

Each of the evidence, panel, and frequency inputs is supplied as exactly one named table/view or ordinary Parquet path. Optional sample selection is exact: every requested ID must occur. Results contain the panel and frequency digests, usable-site denominators, numerical status, and all filter settings.

Value

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

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