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Diffuse seed genes over a network

diffuse_seed_nodes.Rd

This function takes a diffusion vector and leverages personalised page-rank diffusion to identify influential nodes. These can be used subsequently for community detection or check AUROC values given a set of genes.

Usage

diffuse_seed_nodes(
  object,
  diffusion_vector,
  summarisation = c("max", "mean", "harmonic_sum")
)

Arguments

object

NetworkDiffusions object. The underlying class NetworkDiffusions().

diffusion_vector

Named nuermic. A named vector with values to use for the reset parameter in the personalised page-rank diffusion. Names should represent node names of the graph.

summarisation

String. If there are duplicated names in the diffusion_vector how to summarise the scores.

Value

The class with added diffusion score based on a single set of seed genes. Additionally, the seed genes are stored in the class.

Examples

# personalised page-rank diffusion from three seed nodes
set.seed(42)
g <- igraph::sample_pa(15, directed = FALSE)
edges <- data.table::setDT(igraph::as_data_frame(g))[, `:=`(
  from = sprintf("node_%i", from),
  to = sprintf("node_%i", to)
)]
object <- NetworkDiffusions(edges, weighted = FALSE, directed = FALSE)
object <- diffuse_seed_nodes(
  object,
  c(node_1 = 1, node_3 = 1, node_10 = 1),
  summarisation = "max"
)
head(get_diffusion_vector(object))
#>     node_1     node_2     node_3     node_4     node_6     node_7 
#> 0.10750018 0.27058907 0.12650867 0.08945174 0.03667234 0.02975890