GenesNetwork-class: Class "GenesNetwork"

In geNetClassifier: Classify diseases and build associated gene networks using gene expression profiles

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)	

geNetClassifier documentation built on Nov. 8, 2020, 4:53 p.m.