The miner-mechinf tool¶

This utility computes the mechanistic inference.

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

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

miner-mechinf - MINER compute mechanistic inference

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

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

Parameters in detail¶

miner-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

datadir: The path to the data directory

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