networkFeature {BioNetStat} | R Documentation

## 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"))

[Package BioNetStat version 1.12.0 Index]