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Murali-group / Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference
GNU General Public License v3.0
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Lacking of "Type" in ground truth network #43

Closed Hsu-Che-Wei closed 3 years ago

Hsu-Che-Wei commented 3 years ago

Hi Aditya,

I would like to ask what if the ground truth network I have does not have "+" (activation) or "-" (repression). Is it still possible to run evaluation process? I only know that there exist regulation relationship between Gene1 and Gene2, but are not sure about the gene pairs interaction type.

Thank you.

Best, Che-Wei

adyprat commented 3 years ago

Hi, You should be able to use evaluation script without the Type column; most should work except for signed early precision computation. Let me know if you have any difficulty. Best, Aditya

Hsu-Che-Wei commented 3 years ago

Hi Aditya,

When I want to use BLEvaluator.py to estimate AUROC and AUPRC, I found that although there is output files, rankedEdges.csv is missing. Could that because that I didn't finish running the script? I stopped the script when it was running SCRIBE cause it's taking too long (more than 3 days). If that is the case, could you please tell me how can I generate rankedEdges.csv for the rest of the algorithms without rerun the whole process?

Thank you

Best, Che-Wei

adyprat commented 3 years ago

You're right. If you abort an algorithm, it does not create a rankedEdges.csv file. In order to avoid running an algorithm, you can set "should_run: [False]" in the config.yaml file. Hope that helps.