networkFeature: Network features

In BioNetStat: Biological Network Analysis

Description

Network feature average nodes scores (degree, betweenness, closenness, eigenvector centralities or clustering coefficient) or spectral entropies for each network analysed.

Usage

averageDegreeCentrality(expr, labels, adjacencyMatrix, options = NULL)

averageBetweennessCentrality(expr, labels, adjacencyMatrix, options = NULL)

averageBetweennessEdgesCentrality(
  expr,
  labels,
  adjacencyMatrix,
  options = NULL
)

averageClosenessCentrality(expr, labels, adjacencyMatrix, options = NULL)

averageEigenvectorCentrality(expr, labels, adjacencyMatrix, options = NULL)

averageClusteringCoefficient(expr, labels, adjacencyMatrix, options = NULL)

averageShortestPath(expr, labels, adjacencyMatrix, options = NULL)

spectralEntropies(
  expr,
  labels,
  adjacencyMatrix,
  options = list(bandwidth = "Sturges")
)

Arguments

expr	Matrix of variables (columns) vs samples (rows)
labels	a vector in which a position indicates the phenotype of the corresponding sample or state
adjacencyMatrix	a function that returns the adjacency matrix for a given variables values matrix
options	a list containing parameters. Used only in spectralEntropies function. It can be set to either list(bandwidth="Sturges") or list(bandwidth="Silverman").

Value

a list of values containing the spectral entropie or average node score of each network.

spectralEntropies. A list of values containing the spectral entropy of each network.

Examples

set.seed(1)
expr <- as.data.frame(matrix(rnorm(120),40,30))
labels<-data.frame(code=rep(0:3,10),names=rep(c("A","B","C","D"),10))
adjacencyMatrix1 <- adjacencyMatrix(method="spearman", association="pvalue",
 threshold="fdr", thr.value=0.05, weighted=FALSE)

# Average degree centrality
averageDegreeCentrality(expr, labels, adjacencyMatrix1)

# Average betweenness centrality
averageBetweennessCentrality(expr, labels, adjacencyMatrix1)

# Average betweenness centrality
averageBetweennessCentrality(expr, labels, adjacencyMatrix1)

# Average closeness centrality
averageClosenessCentrality(expr, labels, adjacencyMatrix1)

# Average eigenvector centrality
averageEigenvectorCentrality(expr, labels, adjacencyMatrix1)

# Average clustering coefficient
averageClusteringCoefficient(expr, labels, adjacencyMatrix1)

# Average shortest path
averageShortestPath(expr, labels, adjacencyMatrix1)

# Spectral entropies
spectralEntropies(expr, labels, adjacencyMatrix1, options=list(bandwidth="Sturges"))

BioNetStat documentation built on Feb. 3, 2021, 2:01 a.m.