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_edgesoption is recommended instead. (default 0)dummy_mode: one of
terminals,all,others, orfile.terminals: connect the dummy node to all nodes that have been assigned prizesall: 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
Dataset Usage
OmicsIntegrator1 prefers prize``s, but will take the union of ``sources and targets
and set their ‘prize’ to 1 if prize is not specified. If any dummy_nodes are specified,
these are passed to OmicsIntegrator1 and can have their behavior configured with dummy_mode.
OmicsIntegrator1 uses edge direction information.