I'm using the RRHO package to compare ranked gene sets. The associated publication mentions that "the highest intensity point on the [RRHO] map can be used to extract the most statistically significant overlapping gene set", but there is no information on how this is accomplished. How exactly can this be accomplished?

Figured this out...use the output matrix of -log10(Pvalues). Make sure the matrix is oriented the same way that is observed in the RRHO map, then extract the matrix x and y coordinates of the highest intensity point. These will correspond to the rankings from the two gene sets being compared. Then select for all genes from these coordinates to the nearest corner.