rduckhts_munge: Munge Summary Statistics Rows

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

Munge Summary Statistics Rows

Description

Applies the DuckHTS 'duckhts_munge(...)' table macro to rows from a SQL query or table expression, using either an upstream-style preset, a named column map, or a two-column mapping file. When no mapping mode is provided, the bundled 'colheaders.tsv' alias file is used by default.

Usage

rduckhts_munge(
  con,
  query,
  fasta_ref = NULL,
  preset = NULL,
  column_map = NULL,
  column_map_file = NULL,
  iffy_tag = "IFFY",
  mismatch_tag = "REF_MISMATCH",
  ns = NULL,
  nc = NULL,
  ne = NULL
)

Arguments

con	A DuckDB connection with DuckHTS loaded
query	SQL query or table expression to normalize
fasta_ref	Path to the reference FASTA. When NULL (default), operates in fai-only mode: alleles pass through as-is without reference matching or allele swapping, matching upstream '–fai'-only behavior.
preset	Optional preset such as '"PLINK"', '"PLINK2"', '"REGENIE"', '"SAIGE"', '"BOLT"', '"METAL"', '"PGS"', or '"SSF"'
column_map	Optional named character vector mapping canonical munge names such as '"CHR"', '"BP"', '"A1"', '"A2"' to source column names
column_map_file	Optional path to a two-column TSV mapping file in the upstream 'source<TAB>canonical' format
iffy_tag	FILTER tag for ambiguous reference resolution
mismatch_tag	FILTER tag for reference mismatches
ns, nc, ne	Optional global overrides for sample counts

Value

A data frame with normalized GWAS-VCF-style variant/effect columns.

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