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 ...]] [--norm]
[--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 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.
- --norm
Different obs-exp normalization as used by Homer software.
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.
- --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