networkFeature: Network features

In jardimViniciusC/BioNetStat: Biological Network Analysis

Network features

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"))

jardimViniciusC/BioNetStat documentation built on July 3, 2022, 3:32 a.m.