The miner2-bcmembers tool

This utility generates revised coexpression clusters from a gene expression file.

You can see the tool’s available options when you enter miner2-bcmembers -h at the command prompt:

usage: miner2-bcmembers [-h] expfile mapfile regulons outdir

miner2-bcmembers - MINER compute bicluster membership inference

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-bcmembers 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