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 |