The miner3-survival tool

This utility performs survival analysis

You can see the tool’s available options when you enter miner3-survival -h at the command prompt:

usage: miner3-survival [-h] expfile mapfile regulons survfile outdir

miner3-survival - MINER survival analysis

positional arguments:
  expfile       input matrix
  mapfile       identifier mapping file
  networkdir    result directory from miner-mechinf
  survfile      survival data CSV file
  translocfile  mutations CSV file
  outdir        output directory

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

Parameters in detail

miner3-survival expects at least these 4 arguments:

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

  • mapfile: The gene identifier map file.

  • networkdir: The directory containing results generated by the miner-mechinf tool.

  • survfile: The survival data in CSV format

  • translocfile: The mutation 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