rduckhts_depth_region_fraction: Estimate the Share of Cells with a One-Copy Change of a...

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

Estimate the Share of Cells with a One-Copy Change of a Region

Description

For each sample and named region, compares the depth of the region's kept bins with the depth of the sample's other kept autosomal bins: 'ratio = (C_r / E_r) / (C_b / E_b)' with 'C' and 'E' the sums of reads and expected counts, and 'shift = 2 * (ratio - 1)', the share of cells with a one-copy gain (positive) or loss (negative) relative to two copies when the baseline is unchanged. A one-copy change in every cell gives 1 or -1.

Usage

rduckhts_depth_region_fraction(
  con,
  bins_table,
  regions_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 with 'sample_id', 'chrom', 'start', 'end', 'reads', 'expected' and 'kept', such as the output of [rduckhts_depth_bins()].
regions_table	Name of a table or view with 'region', 'chrom', 'start' and 'end' (zero-based, half-open); rows with one name form one region, and a bin belongs to it when its midpoint lies in one of its intervals.
reference_table	Optional name of a table or view of corrected bins of reference samples, in the layout of 'bins_table'.
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', the interval treats bin counts as independent and quasi-Poisson, with the dispersion of the baseline bins, and is 'shift +- 1.959964 shift_se'. With 'reference_table', corrected bins of reference samples, the reported ‘shift' is the sample’s shift minus the mean shift of the references (leaving out the tested sample if it is a reference), and the interval uses Student's t with 'reference_samples - 1' degrees of freedom. Other changes in the sample move the baseline.

Value

A data frame (or invisible 'TRUE' when 'table_name' is given) with one row per sample and region: 'sample_id', 'region', 'bins', 'baseline_bins', 'ratio', 'shift', 'shift_se', 'shift_low', 'shift_high', 'dispersion', 'reference_shift', 'reference_samples', 'status' ('ok', 'no_bins', 'no_baseline' or 'few_reference_samples') and 'method'.

Examples

con <- rduckhts_connect()
DBI::dbExecute(con, paste(
  "CREATE TEMP TABLE bins AS SELECT 'S1' AS sample_id, CAST(c AS VARCHAR) AS chrom,",
  "b * 1000000 AS start, (b + 1) * 1000000 AS \"end\",",
  "0.35 + 0.25 * ((b * 37 + c * 11) % 100) / 100.0 AS gc,",
  "CAST((600 + 4 * ((b * 13 + c * 7) % 11)) *",
  "CASE WHEN c = 8 THEN 1.1 ELSE 1 END AS BIGINT) AS reads",
  "FROM range(1, 23) t(c), range(0, 100) r(b)"
))
rduckhts_depth_bins(con, "bins", table_name = "corrected")
DBI::dbExecute(con, paste(
  "CREATE TEMP TABLE chromosomes AS SELECT CAST(c AS VARCHAR) AS region,",
  "CAST(c AS VARCHAR) AS chrom, 0 AS start, 100000000 AS \"end\" FROM range(1, 23) t(c)"
))
fractions <- rduckhts_depth_region_fraction(con, "corrected", "chromosomes")
fractions[fractions$region == "8", c("region", "shift", "shift_low", "shift_high")]
DBI::dbDisconnect(con, shutdown = TRUE)

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