seeded_rwr: Random walk with restart

In vittoriofortino84/COPS: Clustering algorithms for Omics-driven Patient Stratification

Random walk with restart

Description

Runs random walk in a given network starting from seed genes.

Usage

seeded_rwr(
  X,
  G,
  p = 0.7,
  graph_normalization = c("laplacian", "transition", "none"),
  cholesky = !igraph::is_directed(G),
  affinity_normalization = TRUE
)

Arguments

X	a boolean matrix indicating seeds with samples on columns
G	an igraph.object with nodes matching to rows of X
p	restart probability.
graph_normalization	method used to normalise the adjacency matrix of the input graph.
cholesky	Whether to apply Cholesky decomposition to potentially speed computations. Applicable to undirected graphs.
affinity_normalization	controls whether the output matrix is normalised.

Value

matrix of enrichment scores

vittoriofortino84/COPS documentation built on Jan. 28, 2025, 3:16 p.m.