Influence graph analysis, consistency check, diagnosis, repair and prediction.
Project description
Installation
============
You can install ingranalyze by running::
$ pip install ingranalyze
Usage
=====
Typical usage is::
$ ingranalyze.py --mics --repair 5 networkfile observationfile
For more options you can ask for help as follows:
$ ingranalyze.py -h
usage: ingranalyze.py [-h] [--mics] [--repair {1,2,3,4,5}] [--list_repairs] networkfile observationfile
positional arguments:
networkfile influence graph in bioquali format
observationfile observations in bioquali format
optional arguments:
-h, --help show this help message and exit
--mics compute minimal inconsistent cores
--repair {1,2,3,4,5} choose repair method: 1 flip observed variations, 2
flip influences, 3 define network nodes as inputs, 4
define network nodes as input in an experiment (use
only in case of multiple experiments), 5 add
influences. default is 3
--list_repairs compute all minimal repair sets
Samples
=======
Sample files for yeast are available here:
yeast_guelzim.net_ yeast_snf2.obs_
.. _yeast_guelzim.net: http://bioasp.github.io/downloads/samples/yeastdata/yeast_guelzim.net
.. _yeast_snf2.obs: http://bioasp.github.io/downloads/samples/yeastdata/yeast_snf2.obs
============
You can install ingranalyze by running::
$ pip install ingranalyze
Usage
=====
Typical usage is::
$ ingranalyze.py --mics --repair 5 networkfile observationfile
For more options you can ask for help as follows:
$ ingranalyze.py -h
usage: ingranalyze.py [-h] [--mics] [--repair {1,2,3,4,5}] [--list_repairs] networkfile observationfile
positional arguments:
networkfile influence graph in bioquali format
observationfile observations in bioquali format
optional arguments:
-h, --help show this help message and exit
--mics compute minimal inconsistent cores
--repair {1,2,3,4,5} choose repair method: 1 flip observed variations, 2
flip influences, 3 define network nodes as inputs, 4
define network nodes as input in an experiment (use
only in case of multiple experiments), 5 add
influences. default is 3
--list_repairs compute all minimal repair sets
Samples
=======
Sample files for yeast are available here:
yeast_guelzim.net_ yeast_snf2.obs_
.. _yeast_guelzim.net: http://bioasp.github.io/downloads/samples/yeastdata/yeast_guelzim.net
.. _yeast_snf2.obs: http://bioasp.github.io/downloads/samples/yeastdata/yeast_snf2.obs
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