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.