Hi-C contact probability
I was wondering, if I have a Hi-C matrices and the average ICE-normalized interaction vs. genomic distance, how can I create a plot like the following one?
I created something similar:
but it's not contact probability. I want to draw as well the fractal lineal regression.
I'd like to refer you to Organization of the Mitotic Chromosome, Naumova et al 2013 Science. There is a paragraph about calculating contact probability in supplemental, as well as some references.
I cant see the first image, but from the second, it looks like you would be better off by doing logarithmic binning. I made that plot (and the log-binned one) using code from this tutorial:
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