# 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 ...]]
[--method {dist_norm,lieberman}] [--ligation_factor]
[--extraTrack EXTRATRACK] [--histonMarkType HISTONMARKTYPE]
[--pearsonMatrix PEARSONMATRIX] [--obsexpMatrix OBSEXPMATRIX]


## Required arguments¶

--matrix, -m

HiCExplorer matrix in h5 format.

--outputFileName, -o

File names for the result of the pca.Number of output files 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.

--method

Possible choices: dist_norm, lieberman

possible methods which can be used to build the obs-exp matrix.

Default: “dist_norm”

--ligation_factor

Setting this flag multiplies a scaling factor to each entry of the expected matrix to take care of the proximity ligation as has been explained in Homer software. This flag is only affective with dist_norm method and will be ignored if lieberman method is chosen.

Default: False

--extraTrack

Either a gene track or a histon mark coverage file (preferably a broad mark) is needed to decide if the values of the eigenvector need a sign flip or not.

--histonMarkType

Set it to active or inactive. This is only necessary if a histon mark coverage file is given as an extraTrack.

Default: “active”

--pearsonMatrix, -pm

Internally the input matrix is converted per chromosome to obs_exp matrix and consecutively to a Pearson matrix. Set this parameter to write the pearson matrix to a file.

--obsexpMatrix, -oem

Internally the input matrix is converted per chromosome to obs_exp matrix and consecutively to a Pearson matrix. Set this parameter to write the observe/expected matrix to a file.