Weird results when reproducing some old runs

[lcolladotor]

I'm seeing weird results in Snyder and Hippo when reproducing the results from last year.

Hippo

New:

Old:

Snyder

New:

Old:

Colors of the DERs are not supposed to match perfectly as old versions use q-value < 0.10 and new versions use FWER < 0.05

[lcolladotor]

This is the plot from the BrainSpan data that prompted all of this:

[lcolladotor]

I think I found the culprit.... https://github.com/lcolladotor/derfinder/compare/1c5bc14667fbb6ac23006c7d52474cc6cc3891f3...master#diff-462d1cb76e572011166db2e74da8588fL203

Basically, I changed the default maxRegionGap from 0L to 300L. I should be able to fix the results once the cluster is back online.

[lcolladotor]

Actually, on a second thought fixing the results is not easy. The reason being that the widths and areas from the null regions are going to be incorrect

[lcolladotor]

Script that fixes things as best as possible: https://gist.github.com/bf85e2c7d5d1f8197707

That is, it fixes the regions and annotation. However, the p-values are calculated with the available information from the incorrect null regions. In other words, the p-values are approximated and truly fixing them can only be done by re-running derfinder

[lcolladotor]

Fixed by https://github.com/lcolladotor/derfinder/commit/30ede08171cc97c98b4a8dd6db0e27d50dd0f587

[lcolladotor]

Using https://gist.github.com/c0151c239af76a3972a9 you can visualize the error. Output at https://gist.github.com/56ddebd76a706a931874

Incorrect version:

Correct version: