rduckhts_score: Compute Polygenic Scores
In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

rduckhts_score

R Documentation

Compute Polygenic Scores

Description

Calls the DuckHTS 'bcftools_score(...)' table function to compute sample-level polygenic scores from one genotype VCF/BCF file and one or more summary-statistics files.

Usage

rduckhts_score(
  con,
  bcf_path,
  summary_path = NULL,
  use = NULL,
  columns = "PLINK",
  columns_file = NULL,
  q_score_thr = NULL,
  summaries_list_file = NULL,
  log_path = NULL,
  use_variant_id = FALSE,
  counts = FALSE,
  samples = NULL,
  force_samples = FALSE,
  regions = NULL,
  regions_file = NULL,
  regions_overlap = 1,
  targets = NULL,
  targets_file = NULL,
  targets_overlap = 0,
  apply_filters = NULL,
  include = NULL,
  exclude = NULL
)

Arguments

`con`	A DuckDB connection with DuckHTS loaded
`bcf_path`	Path to genotype VCF/BCF file
`summary_path`	Path(s) to summary-statistics file(s). A character vector computes multiple TSV/SSF PRS columns in one genotype scan. Use 'NULL' with 'summaries_list_file' to read paths from a file.
`use`	Optional dosage source ('"GT"', '"DS"', '"HDS"', '"AP"', '"GP"', '"AS"')
`columns`	Optional summary preset ('"PLINK"', '"PLINK2"', '"REGENIE"', '"SAIGE"', '"BOLT"', '"METAL"', '"PGS"', '"SSF"', '"GWAS-SSF"')
`columns_file`	Optional two-column summary header mapping file
`q_score_thr`	Optional comma-separated p-value thresholds (e.g. '"1e-8,1e-6,1e-4"')
`summaries_list_file`	Optional path to a file (one summary path per line) or directory of summary files, matching upstream 'bcftools +score –summaries'.
`log_path`	Optional path for a matching/audit log with loaded, matched, allele-mismatch, and duplicate-marker counts per PRS.
`use_variant_id`	Logical; if TRUE, match variants by ID instead of CHR+BP
`counts`	Logical; if TRUE, include per-threshold matched-variant counts
`samples`	Optional comma-separated list of sample names to subset (e.g. '"SAMP1,SAMP2"')
`force_samples`	Logical; if TRUE, ignore missing samples instead of erroring
`regions`	Optional comma-separated region list (e.g. '"1:1000-2000,2:50-90"')
`regions_file`	Optional path to a regions file
`regions_overlap`	Overlap mode for regions ('0', '1', or '2'). Default 1 (trim to region).
`targets`	Optional comma-separated targets list
`targets_file`	Optional path to a targets file
`targets_overlap`	Overlap mode for targets ('0', '1', or '2'). Default 0 (record must start in region).
`apply_filters`	Optional comma-separated FILTER names to keep (e.g. '"PASS,."')
`include`	Optional site expression (currently unsupported)
`exclude`	Optional site expression (currently unsupported)