# Classify diseases and build associated gene networks using gene expression profiles

## Documentation for package ‘geNetClassifier’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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"