Classify diseases and build associated gene networks using gene
expression profiles
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Documentation for package ‘geNetClassifier’ version 1.49.0
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" |