The miner2-causalinference tool

This utility computes causal inference and wiring diagrams without using NEO.

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

usage: miner2-causalinference [-h] [--common_mutations COMMON_MUTATIONS]
                              [--translocations TRANSLOCATIONS]
                              [--cytogenetics CYTOGENETICS]
                              expfile mapfile coreg coher outdir

miner-causalinference - MINER causal inference.
MINER Version development (Git SHA 563821013b1f4189d012b54416a7989396d0811d)

positional arguments:
  expfile               input matrix
  mapfile               identifier mapping file
  coreg                 coregulationModules.json file from miner-mechinf
  coher                 coherentMembers.csv file from miner-bcmembers
  outdir                output directory

optional arguments:
  -h, --help            show this help message and exit
  --common_mutations COMMON_MUTATIONS
                        common mutations file
  --translocations TRANSLOCATIONS
                        translocations file
  --cytogenetics CYTOGENETICS
                        cytogenetics file

Parameters in detail

miner2-causalinference expects at least these arguments:

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

• mapfile: The gene identifier map file.

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

• coher: The coherentMembers.csv file generated by the miner-bcmembers tool

• outdir: The directory where the result files will be placed in.

• –common_mutations: The common mutations csv file

• –translocations: The translocations csv file

• –cytogenetics: The cytogenetics csv file

Output in detail

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

• causal_analysis directory containing intermediary results

• completeCausalResults.csv

• wiring_diagram.csv

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