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Munge GWAS Summary Statistics to Align with GDS File

munge_sumstats.Rd

Aligns GWAS summary statistics with a GDS file using chromosome-position or variant ID matching. Performs quality control filtering, allele flipping for discordant variants, and outputs filtered results.

Usage

munge_sumstats(
  gds_path,
  sumstats_path,
  match_by = "CHR-POS",
  chr_col = "CHR",
  pos_col = "POS",
  id_col = "ID",
  ref_col = "REF",
  alt_col = "ALT",
  beta_col = "BETA",
  se_col = "SE",
  af_col = "AF",
  remove_ambiguous = TRUE,
  output_path = NULL
)

Arguments

gds_path

Character; path to the input GDS file.

sumstats_path

Character; path to the GWAS summary statistics file.

match_by

Character; "CHR-POS" (default) or "ID". "CHR-POS": match by chromosome and position (autosomes 1-22 only). "ID": match by variant ID.

chr_col

Character; chromosome column name in the GWAS summary statistics file (default "CHR").

pos_col

Character; position column name in the GWAS summary statistics file (default "POS").

id_col

Character; variant ID column name in the GWAS summary statistics file (default "ID").

ref_col

Character; reference allele column name in the GWAS summary statistics file (default "REF").

alt_col

Character; alternative allele column name in the GWAS summary statistics file (default "ALT").

beta_col

Character; effect size column name in the GWAS summary statistics file (default "BETA").

se_col

Character; standard error column name in the GWAS summary statistics file (default "SE").

af_col

Character; allele frequency column name in the GWAS summary statistics file (default "AF"). Optional; omitted from output if absent in input GWAS summary statistics.

remove_ambiguous

Logical; if TRUE (default), exclude ambiguous SNPs.

output_path

Character or NULL; output file path. If NULL (default), auto-generated as <sumstats_prefix>_munged.txt in the same directory as sumstats_path, where <sumstats_prefix> is the filename prefix of sumstats_path without extension.

Value

Invisibly returns NULL. Filtered results written to output_path as tab-delimited text with columns: CHR, POS, ID, REF, ALT, BETA, SE, AF (optional), GDS_ID. GDS_ID is the 1-based variant index in the input GDS file to match variants in the summary statistics with variants in the GDS file.

Details

Required columns: The input summary statistics must contain columns for REF, ALT, BETA, and SE, along with either (CHR and POS) when match_by = "CHR-POS" or ID when match_by = "ID". The AF column is optional. Additional columns are allowed but ignored. When match_by = "CHR-POS", accepted chromosome formats are autosomes only: 1-22, 01-22, chr1-chr22, or chr01-chr22 (case-insensitive). The BETA column should represent the effect size estimate for the alternative allele (log odds ratio for logistic regression or linear coefficient for linear regression), and the SE column should contain the corresponding standard error.

Quality control filters for summary statistics (applied in order):

  1. REF/ALT: single A/C/G/T nucleotides, biallelic

  2. Ambiguous SNPs: optionally remove A/T, T/A, C/G, G/C

  3. Autosomes: restrict to chromosomes 1-22 (when match_by = "CHR-POS")

  4. POS: POS > 0 (when match_by = "CHR-POS")

  5. ID: non-missing and non-empty (when match_by = "ID")

  6. Duplicates: retain variants with unique (CHR, POS) pairs (when match_by = "CHR-POS") or unique ID (when match_by = "ID")

  7. Effect/SE: BETA != NA, SE > 0

  8. AF range: 0 < AF < 1 (if present)