Harmonize GWAS summary statistics with LD reference

Harmonize GWAS summary statistics with LD reference

harmonize_sumstats_LD(
  sumstats,
  LD_snp_info,
  strand_flip = TRUE,
  remove_strand_ambig = TRUE
)

Arguments

sumstats

A data frame of GWAS summary statistics, including columns "snp" (SNP ID), a0" (reference allele), "a1" (effect allele), "beta", and "zscore".

LD_snp_info

a data frame, SNP info for LD reference, with columns "chrom", "id", "pos", "alt", "ref", "locus" (optional)

strand_flip

Whether to flip signs when reverse complement matches? (default is TRUE).

remove_strand_ambig

Whether to remove ambiguous alleles (A/T and C/G)? (default is TRUE).

Value

a data frame of harmonized GWAS summary statistics