Calls the DuckHTS `bcftools_score(...)` table function to compute sample-level polygenic scores from one genotype VCF/BCF file and one summary-statistics file.
Usage
rduckhts_score(
con,
bcf_path,
summary_path,
use = NULL,
columns = "PLINK",
columns_file = NULL,
q_score_thr = 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 to summary-statistics 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"`)
- 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)