GenesNetwork-class {geNetClassifier} | R Documentation

## Class "GenesNetwork"

### Description

Contains the network returned by `geNetClassifier`. (Slot: `@genesNetwork`)

### Methods

getNodes

  `signature(object = "GenesNetwork")`: Returns the network nodes (genes).

getEdges

  `signature(object = "GenesNetwork")`: Returns the network edges (relationships).

getNumNodes

  `signature(object = "GenesNetwork")`: Returns the number of nodes (genes) in the network.

getNumEdges

  `signature(object = "GenesNetwork")`: Returns the number of edges (relationships) in the network,

getSubNetwork

  `signature(network = "GenesNetwork")`: Returns a new network containing only the given genes.

network2txt

  `signature(network = "GenesNetwork")`: Exports the network as text file.

### Author(s)

Bioinformatics and Functional Genomics Group. Centro de Investigacion del Cancer (CIC-IBMCC, USAL-CSIC). Salamanca. Spain

### See Also

Main package function and classifier training: `geNetClassifier` Plot network or export as iGraph: `plotNetwork`

### Examples

    ######
    # Load data and train a classifier
    ######

    # Load an expressionSet:
    library(leukemiasEset)
    data(leukemiasEset)

    # Select the train samples:
    trainSamples<- c(1:10, 13:22, 25:34, 37:46, 49:58)
    # summary(leukemiasEset$LeukemiaType[trainSamples])

    # Train a classifier or load a trained one:
    # leukemiasClassifier <- geNetClassifier(leukemiasEset[,trainSamples],
    #    sampleLabels="LeukemiaType", plotsName="leukemiasClassifier")
    data(leukemiasClassifier) # Sample trained classifier

    ######
    # Explore the returned object
    ######
    # Global view of the object and its structure:
    names(leukemiasClassifier)

    # List of Networks by classes:
    leukemiasClassifier@genesNetwork
    # Access to the nodes or edges of each network:
    getEdges(leukemiasClassifier@genesNetwork$AML)[1:5,]
    getNodes(leukemiasClassifier@genesNetwork$AML)[1:50]

    ######
    # Plotting
    ######
    # Example: Plotting the sub-network of a class classificationGenes
    # Get the sub-network containing only the classification genes:
    subNet <- getSubNetwork(leukemiasClassifier@genesNetwork,
        leukemiasClassifier@classificationGenes)
    # Get the classification genes' info/details:
    clGenesInfo <- genesDetails(leukemiasClassifier@classificationGenes)

    # Plot the network of the class "ALL"
    plotNetwork(subNet$ALL, genesInfo=clGenesInfo,
        plotOnlyConnectedNodesNetwork=FALSE)

[Package geNetClassifier version 1.34.0 Index]