its p-values are somewhat more strongly correlated with those of the MAGMA analysis (Fig 2). An additional summary statistics analysis (MAGMA-pval-1K) on SNP p-values and using 1,000 Genomes reference data was also performed. This showed less power than PLINK even though it uses the same model at the gene level, suggesting that the difference is due to how the genes are aggregated to gene-sets. One of the key differences in this regard is that PLINK gives larger genes greater weight whereas MAGMA weighs them equally. As such a likely explanation is that the PLINK results are partially driven by a smaller number of large genes, though constructing the intermediate models to verify this is beyond the scope of this paper.
