networkFeature {BioNetStat} | R Documentation |
Network feature average nodes scores (degree, betweenness, closenness, eigenvector centralities or clustering coefficient) or spectral entropies for each network analysed.
averageDegreeCentrality(expr, labels, adjacencyMatrix, options = NULL) averageBetweennessCentrality(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"))
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 |
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.
set.seed(1) expr <- as.data.frame(matrix(rnorm(120),40,30)) labels<-rep(0:3,10) 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 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"))