caspo 1.2

Installation

You can install caspo by running:

$ pip install caspo

Note that you may need root (sudo) access for this. Otherwise, you can use a virtualenv. Before using caspo make sure that R is already installed. The first time you run caspo, CellNOptR will be downloaded and installed in your R environment.

Usage

Typical usage is:

$ caspo.py pkn.sif midas.csv

For more options you can ask for help as follows:

$ caspo.py --help
Usage: caspo.py [options] pkn.sif midas.csv

Options:
  -h, --help           show this help message and exit
  -t T, --tolerance=T  suboptimal enumeration tolerance: 0 <= t <= 0.5
                       (Default to 0)
  -p P, --discrete=P   discretization over the integer interval: [0,10^P]
                       (Default to 2)
  -g, --gtts           compute Global Truth Tables (Default to False). This
                       could take some time for many models.
  -o O, --outdir=O     output directory path (Default to current directory)

Samples

Sample files are available for the prior knowledge network and the phospho-proteomics dataset

Output

By default, the output of caspo will be 4 comma-separated-values files:

• models.csv: Matrix representation of logic models

• frequencies.csv: Frequencies of hyperedges occurrence

• exclusives.csv: Mutual exclusives hyperedges with their corresponding frequencies

• inclusives.csv: Mutual inclusives hyperedges with their corresponding frequencies

When using the -g option, caspo will also output:

• gtt_stats.csv: Basic cluster analysis.

• gtt-%i.csv: Explicit computation of each Global Truth Table