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