Compartment strength between A and B compartments

[katikoshak]

Hello! Thank you for your tool. I have a single question: when I'm running quant_strength_trans.py script I get a tsv file with strength of compartments A and B separately. I wonder whether it's possible to calculate compartment strength between A and B compartments?

Thanks in advance!

[magnitov]

Hi @katikoshak,

The way compartment strength is defined in both our tool and two papers that introduced this metric originally (https://doi.org/10.1016/j.cell.2017.05.004 and https://doi.org/10.1038/nature24281) is dividing the average interactions in your compartment of interest over the interactions between compartments. So, interactions between A and B are used to define the strength of compartments A and B in denominator. Therefore, it would not be possible to define compartment strength between A and B compartments the same way.

What you can do is take the average of AB interactions as the proxy for their strength.

Best,
Mikhail

[katikoshak]

Thanks a lot for the explanation!