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)

Value

vector of propagation values

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.