This function harmonizes the allele coding between an LD reference panel and GWAS/eQTL summary data to ensure consistency in the effect allele (A1) and the other allele (A2). The Z-scores in the GWAS/eQTL summary data are adjusted accordingly if the alleles are flipped.
Usage
allele_harmonise(ref_panel, gwas_data)
Arguments
- ref_panel
A data.frame or data.table representing an LD reference panel. It must contain columns "SNP", "A1" (effect allele), and "A2" (other allele).
- gwas_data
A data.frame or data.table representing GWAS/eQTL summary data. It must contain columns "SNP", "A1", "A2", and "Zscore".
Value
A data.table with harmonized alleles and adjusted Z-scores. The output contains the harmonized alleles from the reference panel and the original alleles from the GWAS/eQTL data as separate columns.