The miner2-riskpredict tool

This utility calculates risk prediction data from its input

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

usage: miner2-riskpredict [-h] [--method METHOD] input outdir

miner-riskpredict - MINER compute risk prediction.
MINER Version development (Git SHA 563821013b1f4189d012b54416a7989396d0811d)

positional arguments:
  input            input specification file
  outdir           output directory

optional arguments:
  -h, --help       show this help message and exit
  --method METHOD  predictor method (decisionTree or xgboost)
   usage: miner2-riskclassifier [-h] [--method METHOD] input outdir

Parameters in detail

miner2-riskpredict expects at least these 2 arguments:

• input: an input specification in JSON format

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

An example input file

{
  "exp": "MATTDATA/expression/IA12Zscore.csv",
  "idmap": "MATTDATA/identifier_mappings.txt",
  "common_mutations": "MATTDATA/mutations/commonMutations.csv",
  "cytogenetics": "MATTDATA/mutations/cytogenetics.csv",
  "translocations": "MATTDATA/mutations/translocationsIA12.csv",
  "coexpression_dictionary": "MATTRESULT/coexpressionDictionary.json",
  "coexpression_modules": "MATTRESULT/coexpressionModules.json",
  "regulon_modules": "MATTRESULT/regulons.json",
  "mechanistic_output": "MATTRESULT/mechanisticOutput.json",
  "regulon_df": "MATTRESULT/regulonDf.csv",
  "overexpressed_members": "MATTRESULT/overExpressedMembers.csv",
  "underexpressed_members": "MATTRESULT/underExpressedMembers.csv",
  "eigengenes": "MATTRESULT/eigengenes.csv",
  "filtered_causal_results": "MATTRESULT/filteredCausalResults.csv",
  "transcriptional_programs": "MATTRESULT/transcriptional_programs.json",
  "transcriptional_states": "MATTRESULT/transcriptional_states.json",
  "primary_survival_data": "MATTDATA/survival/survivalIA12.csv"
}

Output in detail

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

• CoxProportionalHazardsRegulons.csv cox hazard information by regulon

• CoxProportionalHazardsPrograms.csv cox hazard information by program

• plots and curves