analyzeNetwork: Analyze Functional Network

In FGNet: Functional Gene Networks derived from biological enrichment analyses

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

## Not run: 
# 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

## End(Not run)

FGNet documentation built on Nov. 8, 2020, 5:43 p.m.