The miner2-subtypes tool¶
This utility generates sample subtype and related plots
You can see the tool’s available options when you enter miner2-subtypes -h
at the command prompt:
usage: miner2-subtypes [-h] expfile mapfile regulons outdir
miner2-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¶
miner2-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
transcriptional_states.json
transcriptional_programs.json