rduckhts_count_mixture_lowpass: Estimate a Conditional Second-Genome Share from Low-Pass...

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

Estimate a Conditional Second-Genome Share from Low-Pass Counts

Description

Uses first-read and discordant-pair moments with fixed external calibration. This estimator is separate from rduckhts_count_error_fit(). It is suitable for low-pass, cell-free DNA or low-input DNA counts only under the supplied population frequencies and calibration; the share is not an unconditional biological fraction. Matched-frequency unrelated and IBD1 hypotheses can have identical moments and are reported as unresolved.

Usage

rduckhts_count_mixture_lowpass(
  con,
  counts_table,
  seq_error,
  artefact_weight,
  homozygosity_excess,
  block_bases = 1e+07,
  max_depth = 8,
  min_blocks = 30,
  max_blocks = 512,
  max_candidates = 16,
  max_state_bytes = 2^28,
  table_name = NULL,
  overwrite = FALSE
)

Arguments

con	A DuckDB connection with DuckHTS loaded.
counts_table	Table or view containing sample_id, candidate, chrom, one-based pos, ref_count, alt_count, other_count, sample_af and candidate_af. Counts and sample_af must agree across candidates; site keys must be unique within each sample and candidate. Frequencies refer to the counted alternate allele. Sites missing any candidate frequency are unavailable to every candidate of that sample.
seq_error	Required fixed sequencing error in ⁠[0, 0.5)⁠.
artefact_weight	Required fixed uniform-count artefact weight in ⁠[0, 1)⁠.
homozygosity_excess	Required fixed excess of homozygosity in ⁠[0, 1]⁠.
block_bases	Bases per chromosome-local block, at least 1.
max_depth	Maximum ref plus alt depth, 1 to 65535. Deeper sites are excluded; other_count contributes only to QC totals.
min_blocks	Informative blocks required for 95 percent limits, at least 2, default 30. Matched frequencies require pair-bearing blocks; otherwise read-bearing blocks count. Lower values support small-fixture checks, not well-calibrated inference. Below this floor the share is reported but limits are NA and status is insufficient_blocks.
max_blocks	Maximum physical blocks per sample, 1 to 4096.
max_candidates	Maximum candidates per sample, 1 to 64.
max_state_bytes	Maximum bytes of concurrently owned native moment buffers and fit copies. DuckDB owns SQL sorting, materialization and spill.
table_name	Optional output table; otherwise return a data frame.
overwrite	Whether to replace an existing output table.

Value

One row per sample, candidate and relationship model. IBD1 rows require exact candidate_af == sample_af at every input site, including zero-read and excluded sites. Columns include the bounded share (0 to 0.5), block-jackknife standard error and score-inverted limits, singles share, pair residual, relationship diagnostic, QC read/pair totals, calibration, score rank and status. The discordance ratio divides discordant pairs by SUM(choose(depth, 2) * sample_af * (1 - sample_af)). When table_name is supplied, returns invisible TRUE.

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