Comments (2)
Hi @PerrineLacour,
- The default kernel size is used no matter the bin size, if you want you can use
--win-size
to rescale it to a desired size - In theory yes, but in my experience it is not that important. Scaling up x2 should be sufficient.
If you want you can also compare the rescaled kernel visually to loops on your map. To view what the rescaled kernel would look like, you could write this in a python console:
import chromosight.kernels as ck
import chromosight.utils.preprocessing as cup
import matplotlib.pyplot as plt
RESIZE_FACTOR = 5
plt.imshow(cup.resize_kernel(ck.loops['kernels'][0], factor=RESIZE_FACTOR))
plt.show()
Cyril
from chromosight.
Thank you a lot for your answer!
Best,
from chromosight.
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