The miner3-coexpr tool

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

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

usage: miner3-coexpr [-h] [-mg MINGENES] [-moxs MINOVEREXPSAMP]
                     [-mx MAXEXCLUSION] [-rs RANDSTATE] [-oxt OVEREXPTHRESH]
                     expfile mapfile outdir

miner3-coexpr - MINER cluster expression data.

positional arguments:
  expfile               input matrix
  mapfile               identifier mapping file
  outdir                output directory

optional arguments:
  -h, --help            show this help message and exit
  -mg MINGENES, --mingenes MINGENES
                        min number genes
  -moxs MINOVEREXPSAMP, --minoverexpsamp MINOVEREXPSAMP
                        minimum overexpression samples
  -mx MAXEXCLUSION, --maxexclusion MAXEXCLUSION
                        maximum samples excluded
  -rs RANDSTATE, --randstate RANDSTATE
                        random state
  -oxt OVEREXPTHRESH, --overexpthresh OVEREXPTHRESH
                        overexpression threshold

Parameters in detail

miner3-coexpr expects at least these 3 arguments:

  • expfile: The gene expression file a matrix in csv format.

  • mapfile: The gene identifier map file.

  • outdir: The path to the output directory

In addition, you can specify the following optional arguments:

  • --mingenes or --mg: the minimum number of genes in a cluster.

  • --minoverexpsamp or --moxs: minimum number of overexpression samples

  • --maxexclusion or -mx: maximum exclusion

  • --randstate or -rs: random state

  • --overexpthresh or -oxt: overexpression threshold

Output in detail

After successful completion there will be the following files in the output directory

  • cluster_size_distribution.pdf: a plot of the cluster size distribution for visual verification

  • coexpressionDictionary.json: this file is used in subsequent stages