hicCompartmentsPolarization

Rearrange the average interaction frequencies using the first PC values to represent the global compartmentalization signal

$ hicGlobalInteraction –obsexp_matrices obsExpMatrix.h5 –pca pc1.bedgraph -o global_signal.png

usage: hicCompartmentsPolarization [-h] --obsexp_matrices OBSEXP_MATRICES
                                   [OBSEXP_MATRICES ...] --pca PCA
                                   --outputFileName OUTPUTFILENAME
                                   [--quantile QUANTILE] [--outliers OUTLIERS]
                                   [--outputMatrix OUTPUTMATRIX]

Required arguments

--obsexp_matrices, -m

HiCExplorer matrices in h5/cool format.

--pca

a PCA vector as a bedgraph file with no header. In case of several matrices with different conditions, ie. controltreatment, the PCA of control can be used. Note that only one PCA can be provided.

--outputFileName, -o

Plot to represent the polarization of A/B compartments.

Optional arguments

--quantile, -q

number of quantiles

Default: 30

--outliers

precentage of outlier to remove

Default: 0

--outputMatrix

output .npz file includes all the generated matrices