analyzeNetwork {FGNet} | R Documentation

## Analyze Functional Network

### Description

Analyzes the degree and betweenness of the genes in the functional network.

### Usage

    analyzeNetwork(incidMatrices, fNw = NULL, plotOutput = TRUE, colors = NULL)

### Arguments

`incidMatrices` | list or matrix. Output from `fea2incidMat` or the equivalent incidence matrices.
`fNw` | list. Return from `functionalNetwork` to avoid recalculating.
`plotOutput` | logical. Wether to plot the degree and betweenness boxplots.
`colors` | vector. Colors for the metagroups

### Value

List:

- degree, betweenness: Degree and Betweenness of the nodes in the global network (commonClusters) and within each cluster/metagroup (subsets of commonGtSets network). The degree is given as percentage, normalized based on the total number of nodes of the network. i.e. a value of 90 in a network of 10 nodes, would mean the actual degree of the node is 9: it is conneded to 9 nodes (90% of 10)).

- transitivity: Transitivity of the networks.

- betweennessMatrix: Betweenness of each node in each cluster.

- hubsList: Nodes selected as potential hubs in the global network and within each cluster/metagroup (nodes with betweenness over 75% in the given network/subnetwork).

- intraHubsCount: Number of times each node was selected as potential intra-cluster hub.

### See Also

Overview of the package: `FGNet`

Package tutorial: `vignette("FGNet-vignette")`

### Examples

    # Previous Steps
    jobID <- 3907019
    results <- fea_gtLinker_getResults(jobID)
    incidMat <- fea2incidMat(results, filterAttribute="Silhouette Width")

    # Plot node degree and betweensess
    analyzeNetwork(incidMat)

    # Get stats without plotting
    nwStats <- analyzeNetwork(incidMat, plotOutput=FALSE)
    names(nwStats)
    nwStats$hubsTable

[Package FGNet version 3.14.0 Index]