All analyses were performed on the Genetic Cluster Computer, which is part of the Dutch Lisa Cluster. In terms of computational performance MAGMA is shown to have a considerable advantage over the other methods (Table 5) for both gene and gene-set analysis. The most marked difference is between MAGMA and PLINK, the only one of the alternative methods using raw data input. However, the raw data analysis in MAGMA outperforms the summary statistics methods as well. Although INRICH and ALIGATOR show comparable computation times at their lowest SNP p-value cut-off, the need to repeat the analysis at multiple cut-offs means the total analysis for both takes considerably longer.
