net_stats {BioNERO}

R Documentation

Calculate network statistics

Description

Calculate network statistics

Usage

net_stats(
  adj_matrix = NULL,
  net_type = c("gcn", "ppi", "grn"),
  calculate_additional = FALSE
)

Arguments

adj_matrix	Adjacency matrix that represents the network.
net_type	One of "gcn" (gene coexpression network), "ppi" (protein-protein interaction), or "grn" (gene regulatory network).
calculate_additional	Logical indicating whether to calculate additional network statistics (betweenness and closeness). Default is FALSE.

Value

A list containing the following elements:

• Connectivity

• ScaledConnectivity

• ClusterCoef

• MAR (for gcn only)

• Density

• Centralization

• Heterogeneity (gcn only)

• nCliques

• Diameter

• Betweenness

• Closeness

See Also

graph_from_adjacency_matrix, cliques,diameter, estimate_betweenness,V, closeness,degree, transitivity,edge_density, centr_degree fundamentalNetworkConcepts

Examples

data(filt.se)
set.seed(12)
filt.se <- filter_by_variance(filt.se, n=100)
gcn <- exp2gcn(filt.se, SFTpower = 19, cor_method = "pearson",
               net_type = "signed hybrid")
stats <- net_stats(gcn$adjacency_matrix, net_type="gcn")

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