The miner2-causalinference tool
===============================

This utility computes causal inference and wiring diagrams without using
NEO.

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

.. highlight:: none

::

  usage: miner2-causalinference [-h] [--common_mutations COMMON_MUTATIONS]
                                [--translocations TRANSLOCATIONS]
                                [--cytogenetics CYTOGENETICS]
                                expfile mapfile coreg coher outdir

  miner-causalinference - MINER causal inference.
  MINER Version development (Git SHA 563821013b1f4189d012b54416a7989396d0811d)

  positional arguments:
    expfile               input matrix
    mapfile               identifier mapping file
    coreg                 coregulationModules.json file from miner-mechinf
    coher                 coherentMembers.csv file from miner-bcmembers
    outdir                output directory

  optional arguments:
    -h, --help            show this help message and exit
    --common_mutations COMMON_MUTATIONS
                          common mutations file
    --translocations TRANSLOCATIONS
                          translocations file
    --cytogenetics CYTOGENETICS
                          cytogenetics file


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

``miner2-causalinference`` expects at least these arguments:

  * **expfile:** The gene expression file a matrix in csv format.
  * **mapfile:** The gene identifier map file.
  * **coreg:** The coregulationsModules.json file generated by the miner-mechinf tool
  * **coher:** The coherentMembers.csv file generated by the miner-bcmembers tool
  * **outdir:** The directory where the result files will be placed in.
  * **--common_mutations:** The common mutations csv file
  * **--translocations:** The translocations csv file
  * **--cytogenetics:** The cytogenetics csv file

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

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

  * ``causal_analysis`` directory containing intermediary results
  * ``completeCausalResults.csv``
  * ``wiring_diagram.csv``

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