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: msgsteiner reinforcement parameter that affects the convergence of the solution and runtime, with larger values leading to faster convergence but suboptimal results (default 0.001)

  • r: msgsteiner parameter that adds random noise to edges, which is rarely needed because the noisy_edges option is recommended instead. (default 0)

  • dummy_mode: one of terminals, all, others, or file.

    • terminals: connect the dummy node to all nodes that have been assigned prizes

    • all: connect the dummy node to all nodes in the interactome (i.e. full set of nodes in graph)

    • others: connect the dummy node to all nodes that are not terminal nodes (i.e. nodes without prizes)

    • file: connect the dummy node to a specific list of nodes provided in a file