hicHyperoptDetectLoops¶
usage: hicHyperoptDetectLoops --matrix MATRIX --proteinFile PROTEINFILE
--maximumNumberOfLoops MAXIMUMNUMBEROFLOOPS
[--outputFileName OUTPUTFILENAME]
[--resolution RESOLUTION]
[--chrPrefixLoops {None,add,remove}]
[--threads THREADS] [--runs RUNS] [--help]
[--version]
Required arguments¶
- --matrix, -m
The matrix to compute the loops on.
- --proteinFile, -p
The protein file to validate the detected loops
- --maximumNumberOfLoops, -ml
The maximum number of loops that should be used for optimization computation.
- --outputFileName, -o
File names for the result of the optimization (Default: “hyperopt_result.txt”).
Default: “hyperopt_result.txt”
Optional arguments¶
- --resolution, -re
Resolution of matrix (Default: 10000).
Default: 10000
- --chrPrefixLoops, -cl
Possible choices: None, add, remove
Adding / removing / do nothing a ‘chr’-prefix to chromosome name of the loops.
- --threads, -t
Number of threads (uses the python multiprocessing module) (Default: 4).
Default: 4
- --runs, -r
Number of runs of hyperopt (Default: 100).
Default: 100
- --version
show program’s version number and exit