rduckhts_depth_sex_fraction: Estimate the Share of a Second Genome of the Other Sex from X...

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

Estimate the Share of a Second Genome of the Other Sex from X and Y Depth

Description

Treats each sample as a major genome and a second genome of the other sex with a DNA share 'f' below 0.5. 'x_copies' and 'y_copies' are twice the depth ratio of the kept X or Y bins to the kept autosomal bins. For an XX major genome 'x_copies = 2 - f' and 'y_copies = f'; for an XY one 'x_copies = 1 + f' and 'y_copies = 1 - f'. The major genome is XX when 'x_copies >= 1.5'. 'fraction_x' and 'fraction_y' are the two estimates, unclipped; 'fraction' combines them by inverse variance and 'agreement_z' compares them, since an X or Y copy change of the major genome moves them differently.

Usage

rduckhts_depth_sex_fraction(
  con,
  bins_table,
  reference_table = NULL,
  table_name = NULL,
  overwrite = FALSE
)

Arguments

con	A DuckDB connection with DuckHTS loaded.
bins_table	Name of a table or view of corrected bins, as for [rduckhts_depth_region_fraction()].
reference_table	Optional name of a table or view of corrected bins of reference samples with a 'sex' column, 'XX' or 'XY'.
table_name	Optional table to create instead of returning a data frame.
overwrite	Whether 'table_name' may replace an existing table.

Details

Without 'reference_table', one X copy is 1, two are 2, one Y copy is 1 and a genome without Y has no Y depth. With 'reference_table', its XY samples set the depth of one X and one Y copy, and its XX samples, when present, set two X copies and the Y background; the tested sample is left out of its own reference. Remove the pseudo-autosomal regions of X, and Y bins that are not single-copy, in SQL first.

Value

A data frame (or invisible 'TRUE' when 'table_name' is given) with one row per sample: 'sample_id', 'autosomal_bins', 'x_bins', 'y_bins', 'dispersion', 'x_copies', 'x_copies_se', 'y_copies', 'y_copies_se', 'major_sex', 'fraction_x', 'fraction_x_se', 'fraction_y', 'fraction_y_se', 'fraction', 'fraction_se', 'fraction_low', 'fraction_high', 'agreement_z', 'reference_samples', 'status' ('ok', 'no_autosomal_bins', 'no_xy_reference', 'bad_reference', 'no_sex_bins', 'no_x_bins', 'no_y_bins' or 'x_y_disagree') and 'method'.

Examples

con <- rduckhts_connect()
DBI::dbExecute(con, paste(
  "CREATE TEMP TABLE bins AS SELECT 'S1' AS sample_id, chrom,",
  "b * 1000000 AS start, (b + 1) * 1000000 AS \"end\",",
  "0.35 + 0.25 * ((b * 37 + length(chrom) * 11) % 100) / 100.0 AS gc,",
  "CAST((600 + 4 * ((b * 13) % 11)) * CASE chrom WHEN 'X' THEN 0.95 WHEN 'Y' THEN 0.05",
  "ELSE 1 END AS BIGINT) AS reads",
  "FROM (SELECT CAST(c AS VARCHAR) AS chrom FROM range(1, 23) t(c)",
  "UNION ALL SELECT 'X' UNION ALL SELECT 'Y') g, range(0, 60) r(b)"
))
rduckhts_depth_bins(con, "bins", table_name = "corrected")
rduckhts_depth_sex_fraction(con, "corrected")[, c("major_sex", "fraction", "status")]
DBI::dbDisconnect(con, shutdown = TRUE)

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