- Applying PCA to compute the global compartmentalization signal
To our knowledge this method has been first introduced by Wibke Schwarzer et al. 2017 (Nature. 2017 Nov 2; 551(7678): 51–56). In this method, a global (genome-wide) strength for compartmentalization is computed as (AA + BB) / (AB + BA) after rearranging the bins of obs/exp based on their corresponding pc1 values. For this purpose, first pc1 values are reordered incrementally, then the same order of bins is used to rearrange the bins in obs/exp matrix.
$ hicCompartmentsPolarization --obsexp_matrices obsExpMatrix.h5 --pca pc1.bedgraph
-o global_signal.png