when performing the Shuffle within enrichPeakOverlap function, which peaks are being shuffled? the query or the target peak? How the p value is a computed? The source code would be helpful here.

When I interchange the query and target peaks, the output are totally different, could change from significant to non-significant. The same two peaks, just depend on which is feed into the query versus the target, the result changed completely. I would appreciate your insight on this issue. since this issue makes interoperate the result(p.adjust) unreliable.