Gene-set analysis for MAGMA was performed based on the PC regression gene analysis model (MAGMA-main) as well as on the SNP-wise model with 1,000 Genomes reference data (MAGMA-pval-1K). Several other analyses were performed for comparison: PLINK self-contained gene-set analysis without pruning (PLINK-avg) and with pruning (PLINK-prune), as well as ALIGATOR, INRICH and MAGENTA competitive gene-set analysis. PLINK operates on raw genotype data, whereas all three competitive methods require only SNP p-values as input. No correction for stratification was used in any of the analyses except when explicitly specified. An overview of all analyses is given in Table 1.
