joachimwolff
commented
3 years ago Hi Jun,
We do not develop a method like this. However, in the paper they write their P(s) function is inspired by cooltools. I think this documentation can help you to get the P(s) plots you want to have: https://cooltools.readthedocs.io/en/latest/notebooks/contacts_vs_distance.html?highlight=p(s)#Plot-the-P(s)-curve
You can simply take the cool file you used with HiCExplorer and use it with cooltools.
Best,
Joachim
Hi, First, thank you so much for the amazing tool. We recently put a paper on bioarchive, and it couldn't have been possible without this user-friendly tool. I was wondering if you guys are developing a function for getting scaling P(s). source method section: https://www.nature.com/articles/s41556-019-0406-2 Is there much difference between plotDistvsCounts and scaling P(s)? For instance, in the paper the authors mention that the local min/max of derivative of P(s) implies certain properties of loop-extrusion... Is it okay to use DistvsCounts to make similar interpretation? Thank you, Jun