hicAdjustMatrix¶
usage: hicAdjustMatrix --matrix MATRIX --outFileName OUTFILENAME
[--chromosomes CHROMOSOMES [CHROMOSOMES ...]]
[--action {keep,remove,mask}] [--regions REGIONS]
[--help] [--version]
Required arguments¶
–matrix, -m | The matrix to adjust. HiCExplorer supports the following file formats: h5 (native HiCExplorer format) and cool. |
–outFileName, -o | |
File name to save the adjusted matrix. |
Optional arguments¶
–chromosomes, -c | |
List of chromosomes to keep / remove | |
–action | Possible choices: keep, remove, mask Keep, remove or mask the list of specified chromosomes / regions Default: “keep” |
–regions, -r | BED file which stores a list of regions to keep / remove |
–version | show program’s version number and exit |
hicAdjustMatrix can mask, remove or keep defined regions from a BED file or given chromosomes.
Example usages¶
$ hicAdjustMatrix -m matrix.cool --action keep --chromosomes chr1 -o matrix_chr1.cool
$ hicAdjustMatrix -m matrix.cool --action mask --regions mask_regions.bed -o matrix_masked.cool
mask_regions.bed
chr1 10 30
chr1 50 300