Read normalizations included in .(m)cool files

readCoolNorms(file, resolution = NULL)

Arguments

file: A character value specifying the path to the .(m)cool file
resolution: optional, specify which resolution(s) to read normalization types from. Default is all resolutions in `file`.

Value

A vector or list of vectors of available normalizations

Details

The "BALANCE" normalization refers to applying the pre-calculated matrix balancing weights in the `weight` dataset of `file`, typically present in files created using cooler. VC is vanilla coverage, VC_SQRT is square root of vanilla coverage, and KR is Knight-Ruiz normalization.

Please note that if using a file from HiC-Pro, ICE normalizations will come from files stored in a separate folder, and thus will not contain any normalizations explicitly called "ICE" or "BALANCE" since values are included already normalized. This normalization can be specified as "NONE".

Author

Sarah Parker, Nicole Kramer