The miner-subtypes tool

This utility generates sample subtype and related plots

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

usage: miner-subtypes [-h] expfile mapfile regulons outdir

miner-subtypes - MINER compute sample subtypes

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

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

Parameters in detail

miner-subtypes 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.
• 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
• regulon_activity_heatmap.pdf
• centroid_clusters_heatmap.pdf
• regulons_activity_heatmap.csv
• centroidClusters_regulons.pdf
• similarityMatrix_regulons.pdf
• centroids.csv
• states_regulons_0o2_tsne.pdf
• eigengenes.csv
• transcriptional_programs_coexpressionModules - transcriptional programs
• labeled_tsne_kmeans.pdf
• transcriptional_programs_vs_samples.pdf
• labeled_tsne_states.pdf
• tsne_gene_expression.pdf
• programs_vs_states.pdf
• tsne_regulon_activity.pdf