The miner3-subtypes tool

This utility generates sample subtype and related plots

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

usage: miner3-subtypes [-h] expfile mapfile regulons outdir

miner3-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

miner3-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

• coherentMembers.csv

• overExpressedMembers.csv

• underExpressedMembers.csv

• dysregulatedMembers.csv

• overExpressedMembers.json

• underExpressedMembers.json

• 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

• transcriptional_states.json

• transcriptional_programs.json