hicPCA

Computes PCA eigenvectors for a Hi-C matrix.

$ hicPCA –matrix hic_matrix.h5 -o pca1.bedgraph pca2.bedgraph

usage: hicPCA --matrix MATRIX --outputFileName OUTPUTFILENAME
              [OUTPUTFILENAME ...]
              [--numberOfEigenvectors NUMBEROFEIGENVECTORS]
              [--format {bedgraph,bigwig}]
              [--chromosomes CHROMOSOMES [CHROMOSOMES ...]] [--help]
              [--version]

Required arguments

–matrix, -m	HiCExplorer matrix in h5 format.
–outputFileName, -o
	File names for the result of the pca. Number of output file must match the number of computed eigenvectors. Default: [‘pca1’, ‘pca2’]

Optional arguments

–numberOfEigenvectors, -noe
	The number of eigenvectors that the PCA should compute. Default: 2
–format, -f	Possible choices: bedgraph, bigwig output format. Either bedgraph or bigwig. Default: “bigwig”
–chromosomes	List of chromosomes to be included in the correlation.
–version	show program’s version number and exit