MAGMA (v1.06b) 23 is a software for gene-set enrichment analysis using GWAS summary statistics. Briefly, MAGMA computes a gene-level association statistic by averaging P-values of SNPs located around a gene (taking into account LD structure). The gene-level association statistic is then transformed to a Z-value. MAGMA can then be used to test whether a gene set is a predictor of the gene-level association statistic of the trait (Z-value) in a linear regression framework. MAGMA accounts for a number of important covariates such as gene size, gene density, mean sample size for tested SNPs per gene, the inverse of the minor allele counts per gene and the log of these metrics.
