Converts the (interaction) matrix to a observed/expected matrix or a pearson_correlated.

usage: hicTransform --matrix MATRIX --outFileName OUTFILENAME
                    [--method {obs_exp,pearson,covariance,all}]
                    [--chromosomes CHROMOSOMES [CHROMOSOMES ...]]
                    [--threads THREADS] [-help] [--version]

Required arguments

–matrix, -m input file. The computation is done per chromosome.
–outFileName, -o
 File name to save the exported matrix.

Optional arguments

–method, -me

Possible choices: obs_exp, pearson, covariance, all

Transformation method to use. If the option all is used, all three matrices in consecutively way (input -> obs_exp -> pearson -> covariance) are created.

Default: “obs_exp”

–chromosomes List of chromosomes to be included in the correlation.
–threads, -t

Number of threads for pearson correlation.

Default: 4

–version show program’s version number and exit