Hi,

I have read through the regioneR manual and I can't find an explanation of how the y axis values are calculated for the permTestResults plot. I used numOverlap and randomizRegions for my parameters. The x axis is num overlaps. I did notice in the publication that the plots y axis was labeled as 'probability', but I am not sure exactly how the probability was generated and would greatly appreciate an explanation. Thank you for your time   - Patrick

Hi Patrick,

As you say, the x-axis of the perm tests plots depend on the evaluation function, in your case represents the number of overlaps between the two sets of regions.

The y-axis, however, has always the same meaning: the probability density of the evaluation of the randomized region sets. Internally it is created with hist with probability=TRUE. In this mode, the histogram represents the probability density and the histogram has a total area of one.

You can get more information on how the permutation test is performed and how the probability is compiuted in section 3.1 of regioneR's vignette.

If you feel it's not clear enough just ask here and we'll try to clarify.

Hope this helps

Bernat