Introduction to geNetClassifier | Install the package and example data | Main function of the package: geNetClassifier() | External validation: query with new samples of known class | Sample classification: query with new samples of unknown class | Functions to plot the results
Package: geNetClassifier 1.53.0
Sara Aibar
geNetClassifier: Classify diseases and build associated gene networks using gene expression profiles
Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.
Authors:
geNetClassifier_1.53.0.tar.gz
geNetClassifier_1.53.0.zip(r-4.7)geNetClassifier_1.53.0.zip(r-4.6)geNetClassifier_1.53.0.zip(r-4.5)
geNetClassifier_1.53.0.tgz(r-4.6-any)geNetClassifier_1.53.0.tgz(r-4.5-any)
geNetClassifier_1.53.0.tar.gz(r-4.7-any)geNetClassifier_1.53.0.tar.gz(r-4.6-any)
geNetClassifier_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
geNetClassifier/json (API)
| # Install 'geNetClassifier' in R: |
| install.packages('geNetClassifier', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- geneSymbols - Gene symbols associated to human Ensemble IDs.
- leukemiasClassifier - Sample leukemias classifier
On BioConductor:geNetClassifier-1.53.0(bioc 3.24)geNetClassifier-1.52.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
classificationdifferentialexpressionmicroarray
Last updated from:df777b06a6. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 145 | ||
| linux-devel-x86_64 | NOTE | 178 | ||
| source / vignettes | OK | 186 | ||
| linux-release-x86_64 | NOTE | 157 | ||
| macos-release-arm64 | NOTE | 93 | ||
| macos-oldrel-arm64 | NOTE | 123 | ||
| windows-devel | NOTE | 97 | ||
| windows-release | NOTE | 102 | ||
| windows-oldrel | NOTE | 110 | ||
| wasm-release | OK | 105 |
Exports:calculateGenesRankingexternalValidation.probMatrixexternalValidation.statsgClassesgenesDetailsgeNetClassifiergetEdgesgetNodesgetNumEdgesgetNumNodesgetRankinggetSubNetworkgetTopRankinginitializenetwork2txtnumGenesnumSignificantGenesoverviewplot.GenesNetworkplot.GenesRankingplot.GeNetClassifierReturnplotAssignmentsplotDiscriminantPowerplotExpressionProfilesplotNetworkqueryGeNetClassifierquerySummarysetPropertiesshow
Dependencies:BiobaseBiocGenericsclassclustere1071EBarraysgenericsinfotheolatticeMASSminetproxy
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| classify diseases and build associated gene networks using gene expression profiles | geNetClassifier-package |
| Calculate GenesRanking | calculateGenesRanking |
| Probability matrix. | externalValidation.probMatrix |
| Statistics of the external validation. | externalValidation.stats |
| Classes in the ranking. | gClasses gClasses,GenesRanking-method gClasses-methods |
| Class "GeneralizationError" (slot of GeNetClassifierReturn) | GeneralizationError GeneralizationError-class initialize,GeneralizationError-method show,GeneralizationError-method |
| Details of the genes in the network. | genesDetails genesDetails,GenesRanking-method genesDetails-methods genesDetails.GenesRanking |
| Class "GenesNetwork" | GenesNetwork GenesNetwork-class initialize,GenesNetwork-method show,GenesNetwork-method |
| Class "GenesRanking" | extractGenes,GenesRanking-method GenesRanking GenesRanking-class initialize,GenesRanking-method show,GenesRanking-method |
| Gene symbols associated to human Ensemble IDs. | geneSymbols |
| 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. | geNetClassifier |
| Class "GeNetClassifierReturn" | GeNetClassifierReturn GeNetClassifierReturn-class getSlots,GeNetClassifierReturn-method initialize,GeNetClassifierReturn-method names,GeNetClassifierReturn-method show,GeNetClassifierReturn-method |
| Edges in the network. | edges,GenesNetwork-method getEdges getEdges,GenesNetwork-method getEdges-methods |
| Nodes in the network. | getNodes getNodes,GenesNetwork-method getNodes-methods nodes,GenesNetwork-method |
| Number of edges in the network. | getNumEdges getNumEdges,GenesNetwork-method getNumEdges-methods numEdges,GenesNetwork-method |
| Number of nodes in the network. | getNumNodes getNumNodes,GenesNetwork-method getNumNodes-methods numNodes,GenesNetwork-method |
| Shows the genes ranking. | getRanking getRanking,GenesRanking-method getRanking-methods getRanking.GenesRanking |
| Get a sub-network. | getSubNetwork getSubNetwork,GenesNetwork-method getSubNetwork,GeNetClassifierReturn-method getSubNetwork,list-method getSubNetwork,NULL-method getSubNetwork-methods |
| Gets a new ranking with the given top genes. | getTopRanking getTopRanking,GenesRanking-method getTopRanking-methods getTopRanking.GenesRanking |
| Sample leukemias classifier | leukemiasClassifier |
| network2txt | network2txt network2txt,GenesNetwork-method network2txt,list-method network2txt-methods |
| Number of genes in the genesRanking. | numGenes numGenes,GenesRanking-method numGenes-methods |
| Number of ranked genes over the posterior probability threshold. | numSignificantGenes numSignificantGenes,GenesRanking-method numSignificantGenes-methods numSignificantGenes.GenesRanking |
| Overview | overview overview,GeneralizationError-method overview,GenesNetwork-method overview,GenesRanking-method overview,GeNetClassifierReturn-method overview-methods |
| Plot GenesRanking | plot,GenesRanking-method plot.GenesRanking plotGenesRanking |
| Plot GeNetClassifierReturn | plot,GeNetClassifierReturn-method plot.GeNetClassifierReturn plotGeNetClassifierReturn plotGeNetClassifierReturn,GeNetClassifierReturn-method |
| Plot assignment probabilities | plotAssignments |
| Plots the genes' Discriminant Power. | plotDiscriminantPower |
| Expression profiles plot. | plotExpressionProfiles |
| Plot GenesNetwork | plot,GenesNetwork-method plot.GenesNetwork plotNetwork plotNetwork,GenesNetwork-method |
| Queries the classifier trained with geNetClassifier. | queryGeNetClassifier |
| Summary of the query. | querySummary |
| Set properties | setProperties setProperties,GenesRanking-method setProperties-methods setProperties.GenesRanking |