Omics Integrator 1

Omics Integrator 1 is a pathway reconstruction algorithm. See the source code: https://github.com/fraenkel-lab/OmicsIntegrator (licensed under BSD-2), or the associated paper: http://doi.org/10.1371/journal.pcbi.1004879.

OI1 takes some optional arguments:

• noisy_edges: How many times you would like to add noise to the given edge values and re-run the algorithm.

• shuffled_prizes: How many times the algorithm should shuffle the prizes and re-run

• random_terminals: How many times to apply the given prizes to random nodes in the interactome

• seed: the randomness seed to use

• w: float that affects the number of connected components, with higher values leading to more components

• b: the trade-off between including more prizes and using less reliable edges

• d: controls the maximum path-length from root to terminal nodes

• mu: controls the degree-based negative prizes (default 0.0)

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

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

• r: msgsteiner parameter that adds random noise to edges, which is rarely needed. (default 0)