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