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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.

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.