The comparison of competitive methods is somewhat more complicated, due to the fact that ALIGATOR, INRICH and MAGENTA all use discretization using a p-value cut-off. This cut-off needs to be specified by the user and has no obvious default value, although for MAGENTA the 5th percentile cut-off is suggested as the most optimal [12]. For ALIGATOR and INRICH the analysis was therefore performed at four different cut-offs (0.0001, 0.001, 0.005, 0.01), and for MAGENTA at two (5th and 1st percentile).
