The miner2-survival tool

This utility performs survival analysis

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

usage: miner2-survival [-h] expfile mapfile regulons survfile outdir

miner2-survival - MINER survival analysis

positional arguments:
  expfile     input matrix
  mapfile     identifier mapping file
  regulons    regulons.json file from miner-mechinf
  survfile    survival data CSV file
  outdir      output directory

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

Parameters in detail

miner2-survival expects at least these 4 arguments:

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

  • mapfile: The gene identifier map file.

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

  • survfile: The survival data in CSV format

  • 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

  • binaryActivityMap.pdf

  • centroid_clusters_heatmap.pdf

  • Hazards_regression_of_combined_transcriptional_states.csv

  • regulon_activity_heatmap.pdf

  • Risk_groups_boxplot_swarm.pdf

  • Risk_groups_states_.pdf

  • transcriptional_programs_vs_samples.pdf