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:

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