nodeScores {BioNetStat} | R Documentation |
Node score (degree, betweenness, closenness, eigenvector centralities or clustering coefficient) for each network analysed.
degreeCentrality(expr, labels, adjacencyMatrix) betweennessCentrality(expr, labels, adjacencyMatrix) closenessCentrality(expr, labels, adjacencyMatrix) eigenvectorCentrality(expr, labels, adjacencyMatrix) clusteringCoefficient(expr, labels, adjacencyMatrix)
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. |
a list of vector containing the node scores (degree, betweenness, closenness, eigenvector centralities or clustering coefficient) 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) # Degree centrality degreeCentrality(expr, labels, adjacencyMatrix1) # Betweenness Centrality betweennessCentrality(expr, labels, adjacencyMatrix1) # Closenness Caentrality closenessCentrality(expr, labels, adjacencyMatrix1) # Eigenvector centrality eigenvectorCentrality(expr, labels, adjacencyMatrix1) # Clustering coefficient clusteringCoefficient(expr, labels, adjacencyMatrix1)