The miner2-causalinf-post tool
==============================

This utility generates results from the output of the miner2-neo utility

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

.. highlight:: none

::

    usage: miner2-causalinf-post [-h]
                                 expfile mapfile eigengenes neoresults datadir
                                 outdir

    miner2-causalinf-post - MINER post-compute causal inference

    positional arguments:
      expfile     input matrix
      mapfile     identifier mapping file
      eigengenes  eigengenes.csv file generated by miner-causalinf-pre
      mutations   path to mutations CSV file
      neoresults  NEO results directory
      datadir     data directory
      outdir      output directory

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

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

``miner2-causalinf-post`` expects at least these 6 arguments:

  * **expfile:** The gene expression file a matrix in csv format.
  * **mapfile:** The gene identifier map file.
  * **eigengenes:** The eigengenes.csv file created by the miner-causalinf-pre tool
  * **mutations:** A mutations file in CSV format
  * **datadir:** the result directory used for miner-neo
  * **outdir:** The directory where the results of this tool will be stored in

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

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

  * ``regulonCausalMechanisticNetwork.csv``
  * ``regulonNetworkPValues.json``