hicFindEnrichedContacts

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

usage: hicFindEnrichedContacts [-h] --matrix MATRIX --outFileName OUTFILENAME
                               --method {z-score,obs/exp} [--perchr]
                               [--skipDiagonal] [--depth DEPTH] [--version]
optional arguments
--matrix, -m path of the Hi-C matrix.
--outFileName, -o
 File name to save the resulting matrix
--method

Method to transform the matrix values

Possible choices: z-score, obs/exp

--perchr=False Default is to fit distributions per each distance. Setting this option will fit distributions per distance per chromosome
--skipDiagonal=False, -s=False
 If set, diagonal counts are not included
--depth 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