GenesNetwork-class {geNetClassifier} | R Documentation |
Contains the network returned by geNetClassifier
. (Slot: @genesNetwork
)
signature(object = "GenesNetwork")
: Returns the network nodes (genes).
signature(object = "GenesNetwork")
: Returns the network edges (relationships).
signature(object = "GenesNetwork")
: Returns the number of nodes (genes) in the network.
signature(object = "GenesNetwork")
: Returns the number of edges (relationships) in the network,
signature(network = "GenesNetwork")
: Returns a new network containing only the given genes.
signature(network = "GenesNetwork")
: Exports the network as text file.
Bioinformatics and Functional Genomics Group. Centro de Investigacion del Cancer (CIC-IBMCC, USAL-CSIC). Salamanca. Spain
Main package function and classifier training: geNetClassifier
Plot network or export as iGraph: plotNetwork
###### # 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)