The miner-bcmembers tool¶

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

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

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

miner-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¶

miner-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