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: “bedgraph”

–chromosomes List of chromosomes to be included in the correlation.
–version show program’s version number and exit