The K setting determines which partitions have a Minor Arc: a segment with at most K chromosome positions. A Minor Arc p-value is computed from partitions found from Monte Carlo permutations. Large values of K decrease the power of the test, increase search time by K-squared, but render the Major Arc p-values a better fit to the asymptotic formula.
Tip: K is recommended to be 25 or greater, typically 100 at most. Increasing K warrants increasing the number of permutations.
