The miner3-survival tool
========================

This utility performs survival analysis

You can see the tool's available options when you enter ``miner3-survival -h``
at the command prompt:

.. highlight:: none

::

    usage: miner3-survival [-h] expfile mapfile regulons survfile outdir

    miner3-survival - MINER survival analysis

    positional arguments:
      expfile       input matrix
      mapfile       identifier mapping file
      networkdir    result directory from miner-mechinf
      survfile      survival data CSV file
      translocfile  mutations CSV file
      outdir        output directory

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

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

``miner3-survival`` expects at least these 4 arguments:

  * **expfile:** The gene expression file a matrix in csv format.
  * **mapfile:** The gene identifier map file.
  * **networkdir:** The directory containing results generated by the miner-mechinf tool.
  * **survfile:** The survival data in CSV format
  * **translocfile:** The mutation data in CSV format
  * **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

  * ``binaryActivityMap.pdf``
  * ``centroid_clusters_heatmap.pdf``
  * ``Hazards_regression_of_combined_transcriptional_states.csv``
  * ``regulon_activity_heatmap.pdf``
  * ``Risk_groups_boxplot_swarm.pdf``
  * ``Risk_groups_states_.pdf``
  * ``transcriptional_programs_vs_samples.pdf``