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tariks / peakachu

Genome-wide contact analysis using sklearn
MIT License
57 stars 9 forks source link

How to evaluate the detected loops? #14

Closed frankchen121212 closed 2 years ago

frankchen121212 commented 3 years ago

Hello, thank you for the nice work~

I'm interested in how you evaluate your detected loops? In the paper, you mentioned that it was calculated through MCC, ACC, and F1 scores.

However, I still don't understand how you define Acc.

For example, you detected a loop, let's say "loop No.1", so, how would you classify that your detected "loop No.1" into a True Positive detection? From my perspective, I think the detected "loop No.1" should be somehow "close" to the ground truth loop "Ground Truth loop No.1" before it can be classified into a correct detection.

Hope that you could help me thank you!

tariks commented 2 years ago

If I remember correctly, loops were considered close enough to match if they were within 10kb for each coordinate.

frankchen121212 commented 2 years ago

Thank you.