View results

How to use the viewer

Buttons and numbers in the top bar

From left to right:

• Input [Choose file]: load a .json file from WISECONDOR after exporting it through makejson.py.
• Chromosome: the chromosome to show in the plots.
• Scale: the max vertical values in the plots.

Plots

• Z-scores: just as the pdf files produced by plot.py, blue means per bin z-score and red is the Stouffers windowed approach z-score. Calls are marked but not exactly the same as previously: different colors for actual calls and filtered regions are not implemented yet. Orange/brown lines mark the z-score = 3 thresholds.
• Deviation from expectation: The orange line shows how much the bins actual read frequency deviates from the expected value based on the reference set of bins. The value is percentual, meaning a value of 5 is a 5% increase from the expected amount of reads. Green lines show the z-score = 3 thresholds after translating them back to relative percentual differences. For example, a value of 5 means a relative deviation of 5% is required for that bin to be identified as aberrated in the single bin z-score approach.

Call list

• Every call after filtering in WISECONDOR is shown here as a button. You can press the call to directly go to the chromosome the call was made on and select the region found aberrated.

Additional information

• Position: The position selected/the cursor is at.
• Size: Length of the selected region.
• Z-Score: Average z-score over bins in the selected region.
• Z-Stouffers: Recalculated Stouffers z-score. Basically the same as the windowed approach in WISECONDOR, now applied specifically for the selected area to allow varying in size and region for this score.
• Reference Bins (Avg): The average amount of reference bins used for testing bins in the selected region. Low values indicate less reliable results.