In general, methods that compute pathway scores from gene scores assume independence of these scores under the null hypothesis. However, neighbouring genes often have correlated scores due to LD, and are sometimes part of the same pathway. This results in a non-uniform pathway score p-value distribution under the null hypothesis. MAGENTA deals with this problem by pruning gene scores based on LD and using only the highest gene score in the region. However, this introduces a bias toward high gene scores into the calculation of pathway scores[3].
