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 ...]
              [--whichEigenvectors WHICHEIGENVECTORS [WHICHEIGENVECTORS ...]]
              [--format {bedgraph,bigwig}]
              [--chromosomes CHROMOSOMES [CHROMOSOMES ...]]
              [--method {dist_norm,lieberman}] [--ligation_factor]
              [--extraTrack EXTRATRACK] [--histonMarkType HISTONMARKTYPE]
              [--pearsonMatrix PEARSONMATRIX] [--obsexpMatrix OBSEXPMATRIX]
              [--ignoreMaskedBins] [--help] [--version]

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.

Optional arguments

--whichEigenvectors, -we

The list of eigenvectors that the PCA should compute e.g. 1 2 5 will return the first, second and fifth eigenvector. (Default: “1 2”).

Default: “1 2”

--format, -f

Possible choices: bedgraph, bigwig

Output format. Either bedgraph or bigwig (Default: “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 are dist_norm and lieberman (Default: “dist_norm”).

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 histone mark coverage file (preferably a broad mark) is needed to decide if the values of the eigenvector need a sign flip or not. Please consider: bed files are interpreted as gene tracks and bigwig files as histone marks.

--histonMarkType

Set it to active or inactive. This is only necessary if a histon mark coverage file is given as an extraTrack (Default: “active”).

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.

--ignoreMaskedBins

Mask bins are usually set to 0. This option removes the masked bins before the PCA is computed. Attention: this will lead to empty PCA regions.

Default: False

--version

show program’s version number and exit