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GWAS summary QC pipeline (chip + imputed)

leo.gwas_qc.Rd

Perform QC on GWAS summary stats by merging imputed and genotyped data, removing duplicates, checking consistency, matching to a reference panel, filtering by DAF/F_U cutoffs, and saving results.

Usage

leo.gwas_qc(
  summary_x2_p,
  summary_x2_chip_p,
  ref_p = "/Users/leoarrow/Project/ref/1kg_maf/zuo_ref/1KG-EAS-EAF-chrposa2a1.txt.gz",
  save_dir = "~/Project/BD2025/data/qc/sex_split",
  save_name_prefix = "bd-ASA-41",
  DAF_cutoff = 0.2,
  F_U_cutoff = 0.01
)

Arguments

summary_x2_p

Path to imputed summary file (.assoc/.gz).

summary_x2_chip_p

Path to genotyped (chip) summary file.

ref_p

Path to reference panel or loaded df

save_dir

Output directory (default: "~/Project/BD2025/data/qc/sex_split").

save_name_prefix

Prefix for output file names.

DAF_cutoff

Numeric. Max |DAF| allowed (default 0.2).

F_U_cutoff

Numeric. Min F_U required (default 0.01).

Value

return(summary_qc); writes QC results to save_dir.

Details

Major steps:

  • Read and standardize imputed & chip data

  • Remove duplicates (keep smallest P for genotyped, drop multiple imputed)

  • Merge and label GI (imputed/genotyped)

  • Match with reference panel and compute DAF

  • Filter by cutoffs and save full / P<1e-6 subsets and output

Logs at each step with leo_log() for dimension, duplication, NA, etc.

Examples

if (FALSE) { # \dontrun{
leo.gwas_qc("imp.assoc.gz", "chip.assoc")
} # }