Filter and Align GWAS Data to a Reference Panel

The filter_align function processes a list of GWAS summary statistics data frames, harmonizes alleles according to a reference panel, removes duplicates, and aligns data to common SNPs. It's used to prepare data for further analysis such as LDSC.

Usage

filter_align(gwas_data_list, ref_panel, allele_match = TRUE)

Arguments

gwas_data_list

A list of data.frames where each data.frame contains GWAS summary statistics for a trait. Each data.frame should include columns for SNP identifiers, Z-scores of effect size estimates, sample sizes (N), effect allele (A1), and reference allele (A2).

ref_panel

A data.frame containing the reference panel data. It must include columns for SNP, A1, and A2.

allele_match

Logical. Whether to match alleles. Default TRUE.

Value

A list of data.frames, each corresponding to an input GWAS summary statistics data frame, but filtered, harmonized, and aligned to the common SNPs found across all data frames.

Details

The function performs several key steps: adjusting alleles according to a reference panel, removing duplicate SNPs, and aligning all GWAS data frames to a set of common SNPs. This is often a necessary preprocessing step before performing genetic correlation and heritability analyses.