| network_propagation {PANACEA} | R Documentation |
Network Propagation (Random-walk with Restart)
Description
Network Propagation (Random-walk with Restart)
Usage
network_propagation(prior_vec, W_prime, alpha, max.iter = 1000, eps = 1e-04)
Arguments
prior_vec |
vector of prior knowledge on selected genes (names are gene symbols) |
W_prime |
(Laplacian-normalized, symmetric) adjacency matrix |
alpha |
restart parameter, controlling trade-off between prior information and network smoothing |
max.iter |
maximum allowed number of iterations (default = 1000) |
eps |
epsilon value to assess the L2 norm of the difference between iterations (default = 1e-4) |
Details
Implementing RWR following the following publications: Cowen L, Ideker T, Raphael BJ, Sharan R. Network propagation: a universal amplifier of genetic associations. Nat Rev Genet. 2017 Sep;18(9):551–62. Shnaps O, Perry E, Silverbush D, Sharan R. Inference of personalized drug targets via network propagation. Pac Symp Biocomput. 2016;21:156–67.
Value
vector of propagation values