hicTransform

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