RWR

RWR, or random walk with restarts, is a source and target independent pathway reconstruction algorithm that performs PathRank on the input interactome, using the provided prizes.

For a random walk with restarts implementation that uses sources and targets, see STRWR. RWR takes in two parameters:

• threshold: The number of nodes to have in the final returned subgraph.

• alpha: The damping factor of the internal PathRank algorithm. This is the probability that RWR randomly chooses a neighbor instead of restarting.

RWR is implemented at https://github.com/reed-compbio/rwr.

Dataset Usage

RWR considers the union of sources and targets as the input active nodes. Input interactome directionality is considered, and the output subnetwork is also directed.

Implementation Details

RWR returns a ranked list of nodes: SPRAS returns the induced subgraph from the number of nodes corresponding to the user-specified threshold.

Internally, RWR only takes in directed graphs. SPRAS will automatically convert edges to directed edges as necessary. For more information, see the section on algorithm directionality.