Choosing matrix normalization method for .cool files

[rikrdo89]

For cool files that have values for different types of matrix normalization (KR, VC, VC_SQRT, etc), is there a way to specify which normalization values to use? I tried /path/to/file.cool::/resolutions/5000::/bins/KR but that didn't workl...

resolutions
     ├── 5000
     │   ├── bins
     │   │   ├── KR (617665,) float64
     │   │   ├── VC (617665,) float64
     │   │   ├── VC_SQRT (617665,) float64
     │   │   ├── chrom (617665,) int32
     │   │   ├── end (617665,) int32
     │   │   ├── start (617665,) int32
     │   │   └── weight (617665,) float64
     │   ├── chroms
     │   │   ├── length (24,) int32
     │   │   └── name (24,) |S64
     │   ├── indexes
     │   │   ├── bin1_offset (617666,) int64
     │   │   └── chrom_offset (25,) int64
     │   └── pixels
     │       ├── bin1_id (495409844,) int64
     │       ├── bin2_id (495409844,) int64
     │       └── count (495409844,) int32

[lldelisle]

Hi,
This is a good idea of enhancement (but needs to modify the package we depends on: HiCMatrix). For the moment, we do not support it so you need to use hicConvertFormat to extract the values with the normalization you want. You need to pay attention to the argument --correction_division depending where your matrix comes from. If you need help with this, I can help you.