The null hypothesis in these tests is that the site did not change binding affinity. Low p-value/FDR value indicate confidence that this is no true -- that there is a change. Higher p-value/FDR values,on the other hand, do not indicate confidence that the sites did not change, only that there is not sufficient evidence to be confident that a change occurred. Bottom line: this tool can not be used to test for unchanged site.
If you want to see sites with low fold-changes, you should set th=1 in the call to dba.report() to retrieve all the binding sites. Then you can filter by low Fold changes and higher FDR. You can then sort to see the lowest fold changes first. Here's an example:
Thanks Rory!! This is very helpful solution!