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.