Omics Integrator 2

Omics Integrator 2 is a pathway reconstruction algorithm. See the source code: https://github.com/fraenkel-lab/OmicsIntegrator2 (licensed under BSD-3).

OI2 takes a few optional arguments:

• output_file: the name of the output file, which will overwrite any existing file with this name

• w: (Omega) the weight of the edges connecting the dummy node to the nodes selected by dummyMode (default: 6)

• b: (Beta) scaling factor of prizes (default: 1)

• g: (Gamma) multiplicative edge penalty from degree of endpoints (default: 20)

• noise: Standard Deviation of the gaussian noise added to edges in Noisy Edges Randomizations.

• noisy_edges: An integer specifying how many times to add noise to the given edge values and re-run.

• random_terminals: An integer specifying how many times to apply your given prizes to random nodes in the interactome and re-run

• dummy_mode: Tells the program which nodes in the interactome to connect the dummy node to. (default: terminals)

  • “terminals” = connect to all terminals

  • “others” = connect to all nodes except for terminals

  • “all” = connect to all nodes in the interactome.

• seed: The random seed to use for this run.