Classify diseases and build associated gene networks using gene expression profiles


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Documentation for package ‘geNetClassifier’ version 1.36.0

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geNetClassifier-package classify diseases and build associated gene networks using gene expression profiles
calculateGenesRanking Calculate GenesRanking
edges-method Edges in the network.
externalValidation.probMatrix Probability matrix.
externalValidation.stats Statistics of the external validation.
extractGenes-method Class "GenesRanking"
gClasses Classes in the ranking.
gClasses-method Classes in the ranking.
gClasses-methods Classes in the ranking.
GeneralizationError Class "GeneralizationError" (slot of GeNetClassifierReturn)
GeneralizationError-class Class "GeneralizationError" (slot of GeNetClassifierReturn)
genesDetails Details of the genes in the network.
genesDetails-method Details of the genes in the network.
genesDetails-methods Details of the genes in the network.
genesDetails.GenesRanking Details of the genes in the network.
GenesNetwork Class "GenesNetwork"
GenesNetwork-class Class "GenesNetwork"
GenesRanking Class "GenesRanking"
GenesRanking-class Class "GenesRanking"
geneSymbols Gene symbols associated to human Ensemble IDs.
geNetClassifier Main function of the geNetClassifier package. Trains the multi-class SVM classifier based on the given gene expression data through transparent detection of gene markers and their associated networks.
GeNetClassifierReturn Class "GeNetClassifierReturn"
GeNetClassifierReturn-class Class "GeNetClassifierReturn"
getEdges Edges in the network.
getEdges-method Edges in the network.
getEdges-methods Edges in the network.
getNodes Nodes in the network.
getNodes-method Nodes in the network.
getNodes-methods Nodes in the network.
getNumEdges Number of edges in the network.
getNumEdges-method Number of edges in the network.
getNumEdges-methods Number of edges in the network.
getNumNodes Number of nodes in the network.
getNumNodes-method Number of nodes in the network.
getNumNodes-methods Number of nodes in the network.
getRanking Shows the genes ranking.
getRanking-method Shows the genes ranking.
getRanking-methods Shows the genes ranking.
getRanking.GenesRanking Shows the genes ranking.
getSlots-method Class "GeNetClassifierReturn"
getSubNetwork Get a sub-network.
getSubNetwork-method Get a sub-network.
getSubNetwork-methods Get a sub-network.
getTopRanking Gets a new ranking with the given top genes.
getTopRanking-method Gets a new ranking with the given top genes.
getTopRanking-methods Gets a new ranking with the given top genes.
getTopRanking.GenesRanking Gets a new ranking with the given top genes.
initialize-method Class "GeNetClassifierReturn"
initialize-method Class "GeneralizationError" (slot of GeNetClassifierReturn)
initialize-method Class "GenesNetwork"
initialize-method Class "GenesRanking"
leukemiasClassifier Sample leukemias classifier
names-method Class "GeNetClassifierReturn"
network2txt network2txt
network2txt-method network2txt
network2txt-methods network2txt
nodes-method Nodes in the network.
numEdges-method Number of edges in the network.
numGenes Number of genes in the genesRanking.
numGenes-method Number of genes in the genesRanking.
numGenes-methods Number of genes in the genesRanking.
numNodes-method Number of nodes in the network.
numSignificantGenes Number of ranked genes over the posterior probability threshold.
numSignificantGenes-method Number of ranked genes over the posterior probability threshold.
numSignificantGenes-methods Number of ranked genes over the posterior probability threshold.
numSignificantGenes.GenesRanking Number of ranked genes over the posterior probability threshold.
overview Overview
overview-method Overview
overview-methods Overview
plot-method Plot GeNetClassifierReturn
plot-method Plot GenesRanking
plot-method Plot GenesNetwork
plot.GenesNetwork Plot GenesNetwork
plot.GenesRanking Plot GenesRanking
plot.GeNetClassifierReturn Plot GeNetClassifierReturn
plotAssignments Plot assignment probabilities
plotDiscriminantPower Plots the genes' Discriminant Power.
plotExpressionProfiles Expression profiles plot.
plotGenesRanking Plot GenesRanking
plotGeNetClassifierReturn Plot GeNetClassifierReturn
plotGeNetClassifierReturn-method Plot GeNetClassifierReturn
plotNetwork Plot GenesNetwork
plotNetwork-method Plot GenesNetwork
queryGeNetClassifier Queries the classifier trained with geNetClassifier.
querySummary Summary of the query.
setProperties Set properties
setProperties-method Set properties
setProperties-methods Set properties
setProperties.GenesRanking Set properties
show-method Class "GeNetClassifierReturn"
show-method Class "GeneralizationError" (slot of GeNetClassifierReturn)
show-method Class "GenesNetwork"
show-method Class "GenesRanking"