harmonize_sumstats_LD: Harmonize GWAS summary statistics with LD reference

In kevinlkx/mapgen: Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

Harmonize GWAS summary statistics with LD reference

Description

Harmonize GWAS summary statistics with LD reference

Usage

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

kevinlkx/mapgen documentation built on March 31, 2024, 11:03 p.m.