The miner2-mechinf tool

This utility computes the mechanistic inference.

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

usage: miner2-mechinf [-h] [-mc MINCORR]
                      expfile mapfile coexprdict outdir

miner2-mechinf - MINER compute mechanistic inference

positional arguments:
  expfile               input matrix
  mapfile               identifier mapping file
  coexprdict            coexpressionDictionary.json file from miner-coexpr
  outdir                output directory

optional arguments:
  -h, --help            show this help message and exit
  -mc MINCORR, --mincorr MINCORR
                        minimum correlation

Parameters in detail

miner2-mechinf expects at least these 5 arguments:

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

• mapfile: The gene identifier map file.

• coexprdict: The path coexpressionDictionary.json file from the miner-coexpr tool

• outdir: The path to the output directory

In addition, you can specify the following optional arguments:

• --mincorr or --mc: the minimum correlation value.

Output in detail

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

• regulons.json - use this file in subsequent tools

• coexpressionDictionary_annotated.json

• mechanisticOutput.json

• coexpressionModules_annotated.json

• regulons_annotated.csv

• coexpressionModules.json

• regulons_annotated.json

• coregulationModules.json