The miner2-bcmembers tool
==========================

This utility generates revised coexpression clusters from a gene expression
file.

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

.. highlight:: none

::

    usage: miner2-bcmembers [-h] expfile mapfile regulons outdir

    miner2-bcmembers - MINER compute bicluster membership inference

    positional arguments:
      expfile     input matrix
      mapfile     identifier mapping file
      regulons    regulons.json file from miner-mechinf
      outdir      output directory

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


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

``miner2-bcmembers`` expects at least these 4 arguments:

  * **expfile:** The gene expression file a matrix in csv format.
  * **mapfile:** The gene identifier map file.
  * **regulons:** The regulons.json file generated by the miner-mechinf tool.
  * **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

  * ``coherentMembers.csv``
  * ``overExpressedMembers.csv``
  * ``underExpressedMembers.csv``
  * ``dysregulatedMembers.csv``
  * ``overExpressedMembers.json``
  * ``underExpressedMembers.json``