Pearson correlation matrix

[BenxiaHu]

hello, I have a question on pearson correlation matrix (https://hicexplorer.readthedocs.io/en/latest/content/example_usage.html#a-b-compartment-analysis): how to you calculate the correlation for bewteen 2 loci (such as 100kb) per chromosome? Becasue each locus has only one value (obs/exp), I do not understand why HiCExploer can get the correlation for each locus. Looking forward to your reply!

https://hicexplorer.readthedocs.io/en/latest/content/example_usage.html#a-b-compartment-analysis

[kalavattam]

You can find the answer in this 2009 publication, among others.