hicFindEnrichedContacts

Identifies enriched contacts by computing a observe vs. expected or a z-score matrix

usage: hicFindEnrichedContacts --matrix MATRIX --outFileName OUTFILENAME
                               --method {z-score,obs/exp} [--perchr]
                               [--skipDiagonal] [--maxDepth MAXDEPTH] [--help]
                               [--version]

Required arguments

–matrix, -m	Input matrix.
–outFileName, -o
	File name to save the resulting matrix.
–method	Possible choices: z-score, obs/exp Method to transform the matrix values.

Optional arguments

–perchr	Default is to fit distributions per each distance. Setting this option will fit distributions per distance per chromosome. Default: False
–skipDiagonal, -s
	If set, diagonal counts are not included. Default: False
–maxDepth	Depth (in base pairs) up to which the computations will be carried out. A depth of 10.0000 bp means that any computations involving bins that are over 10kbp apart are not considered.
–version	show program’s version number and exit