The miner2-causalinf-pre tool

This utility generates the input parameters for the miner2-neo utility

You can see the tool’s available options when you enter miner2-causalinf-pre -h at the command prompt:

usage: miner2-causalinf-pre [-h]
                            expfile mapfile mechout coexp coreg mutation
                            datadir outdir

miner2-causalinf-pre - MINER pre-compute causal inference

positional arguments:
  expfile     input matrix
  mapfile     identifier mapping file
  mechout     mechanisticOutput.json file from miner-mechinf
  coexp       coexpressionModules.json file from miner-mechinf
  coreg       coregulationModules.json file from miner-mechinf
  mutation    mutations csv file
  datadir     data directory
  outdir      output directory

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

Parameters in detail

miner2-causalinf-pre expects at least these 8 arguments:

• expfile: The gene expression file a matrix in csv format.

• mapfile: The gene identifier map file.

• mechout: The mechanisticOutput.json file generated by the miner-mechinf tool

• coexp: The coexpressionModules.json file generated by the miner-mechinf tool

• coreg: The coregulationsModules.json file generated by the miner-mechinf tool

• mutations: The mutations CSV file

• datadir: a directory containing “all_tfs_to_motifs.pkl”

• 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

• bcTfIncidence.csv

• filteredMutations.csv

• tfExpression.csv

• eigengenes.csv

• regStratAll.csv

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