The miner2-causalinf-pre tool
=============================

This utility generates the input parameters for the miner2-neo utility

You can see the tool's available options when you enter ``miner2-causalinf-pre -h``
at the command prompt:

.. highlight:: none

::

    usage: miner2-causalinf-pre [-h]
                                expfile mapfile mechout coexp coreg mutation
                                datadir outdir

    miner2-causalinf-pre - MINER pre-compute causal inference

    positional arguments:
      expfile     input matrix
      mapfile     identifier mapping file
      mechout     mechanisticOutput.json file from miner-mechinf
      coexp       coexpressionModules.json file from miner-mechinf
      coreg       coregulationModules.json file from miner-mechinf
      mutation    mutations csv file
      datadir     data directory
      outdir      output directory

    optional arguments:
      -h, --help  show this help message and exit

Parameters in detail
--------------------

``miner2-causalinf-pre`` expects at least these 8 arguments:

  * **expfile:** The gene expression file a matrix in csv format.
  * **mapfile:** The gene identifier map file.
  * **mechout:** The mechanisticOutput.json file generated by the miner-mechinf tool
  * **coexp:** The coexpressionModules.json file generated by the miner-mechinf tool
  * **coreg:** The coregulationsModules.json file generated by the miner-mechinf tool
  * **mutations:** The mutations CSV file
  * **datadir:** a directory containing "all_tfs_to_motifs.pkl"
  * **outdir:** The directory where the result files will be placed in.

Output in detail
----------------

After successful completion there will be the following files in the output directory

  * ``bcTfIncidence.csv``
  * ``filteredMutations.csv``
  * ``tfExpression.csv``
  * ``eigengenes.csv``
  * ``regStratAll.csv``

These files are used as the input to the tool miner-neo