Clean GWAS summary statistics with tidyGWAS — clean

Harmonises column headers via harmonize_sumstats_headers(), applies a minor-allele frequency pre-filter (EFF_ALL_FREQ between 0.001 and 0.999), and passes the result through tidyGWAS::tidyGWAS() for full QC. The tidyGWAS log file is copied to logging_path.

Usage

clean_gwas(sumstats_file, logging_path, column_map = NULL, ...)

Arguments

sumstats_file: Path to a raw GWAS summary statistics file (plain text or .gz).
logging_path: Directory where the tidyGWAS log file will be saved.
column_map: Optional named character vector of per-cohort column renames passed to harmonize_sumstats_headers(). Default NULL.
...: Additional arguments forwarded to tidyGWAS::tidyGWAS().

Value

The cleaned summary statistics object returned by tidyGWAS::tidyGWAS().

Details

Clean GWAS summary statistics

Examples

if (FALSE) { # \dontrun{
cleaned <- clean_gwas(
  sumstats_file = "my_gwas.txt.gz",
  logging_path  = "logs/"
)
} # }