hicAdjustMatrix¶
This tool adjusts hic matrices by keeping, removing or masking a given list of regions or chromosmes.
usage: hicAdjustMatrix --matrix MATRIX --outFileName OUTFILENAME
[--chromosomes CHROMOSOMES [CHROMOSOMES ...] |
--regions REGIONS | --maskBadRegions MASKBADREGIONS]
[--action {keep,remove,mask}]
[--interIntraHandling {None,inter,intra}] [--help]
[--version]
Named Arguments¶
- --chromosomes, -c
List of chromosomes to keep/remove.
- --regions, -r
BED file which stores a list of regions to keep/remove.
- --maskBadRegions, -mbr
Bad regions are identified and masked.
Required arguments¶
- --matrix, -m
The Hi-C 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¶
- --action, -a
Possible choices: keep, remove, mask
Keep, remove or mask the list of specified chromosomes/regions. keep/remove: These options keep/remove bins of matrix by deleting them. This may cause issue plotting the matrix if several parts of a single chromosome are going to be deleted. In that case, one may consider using the mask option (Default: “keep”).
Default: “keep”
- --interIntraHandling, -iih
Possible choices: None, inter, intra
Remove the inter- or intra-chromosomal contacts of the given chromosomes. (Default: None).
- --version
show program’s version number and exit
hicAdjustMatrix can mask, remove or keep defined regions from a BED file or given chromosomes. This can be useful to create a smaller Hi-C matrix of a single chromosome for e.g. testing purposes or to remove repetitive chromosome ends before calculating A/B compartments using hicPCA.
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