net_stats: Calculate network statistics

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

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)

• 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 <- exp_preprocess(
    filt.se, Zk_filtering = FALSE, variance_filter = TRUE, n = 200
)
gcn <- exp2gcn(
    filt.se, SFTpower = 7, cor_method = "pearson", net_type = "signed hybrid"
)
stats <- net_stats(gcn$adjacency_matrix, net_type = "gcn")

almeidasilvaf/BioNERO documentation built on March 25, 2024, 9:14 p.m.