Package: geneClassifiers 1.37.0
R Kuiper
geneClassifiers: Application of gene classifiers
This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.
Authors:
geneClassifiers_1.37.0.tar.gz
geneClassifiers_1.37.0.zip(r-4.7)geneClassifiers_1.37.0.zip(r-4.6)geneClassifiers_1.37.0.zip(r-4.5)
geneClassifiers_1.37.0.tgz(r-4.6-any)geneClassifiers_1.37.0.tgz(r-4.5-any)
geneClassifiers_1.37.0.tar.gz(r-4.7-any)geneClassifiers_1.37.0.tar.gz(r-4.6-any)
geneClassifiers_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
geneClassifiers/json (API)
NEWS
| # Install 'geneClassifiers' in R: |
| install.packages('geneClassifiers', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rkuiper/geneclassifiers/issues
- exampleMAS5 - Example MAS5.0 ExpressionSet
On BioConductor:geneClassifiers-1.37.0(bioc 3.24)geneClassifiers-1.36.0(bioc 3.23)
geneexpressionbiomedicalinformaticsclassificationsurvivalmicroarray
Last updated from:47dc1489c5. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 129 | ||
| linux-devel-x86_64 | NOTE | 146 | ||
| source / vignettes | OK | 168 | ||
| linux-release-x86_64 | NOTE | 186 | ||
| macos-release-arm64 | NOTE | 93 | ||
| macos-oldrel-arm64 | NOTE | 91 | ||
| windows-devel | NOTE | 91 | ||
| windows-release | NOTE | 87 | ||
| windows-oldrel | NOTE | 77 | ||
| wasm-release | OK | 98 |
Exports:getBatchCorrectiongetCitationsgetClassificationsgetClassifiergetDecisionBoundariesgetDescriptiongetEventChaingetInterceptgetMeansgetNamegetNormalizationMethodgetNormalizationMethodsgetProbeNamesgetScoresgetSdsgetTargetValuegetTrainingDatagetWeightingTypegetWeightingTypesgetWeightsrunClassifiersetNormalizationMethodshowClassifierList
Dependencies:BiobaseBiocGenericsgenerics
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract | bracket,FixedExpressionData-method [,FixedExpressionData,ANY,ANY-method [,FixedExpressionData,ANY,missing-method [,FixedExpressionData,missing,ANY-method [[,FixedExpressionData,ANY,ANY-method [[,FixedExpressionData,ANY,missing-method [[,FixedExpressionData,missing,ANY-method |
| An S4 class to store classifier parameters. | ClassifierParameters |
| An S4 class to store classifier results. | ClassifierResults |
| Dimensions of an Object | dim,FixedExpressionData-method |
| Example MAS5.0 ExpressionSet | exampleMAS5 |
| An S4 class to store classifier parameters. | FixedExpressionData |
| Obtain the batch correction status for a classifier result. | getBatchCorrection getBatchCorrection,ClassifierResults-method |
| Obtain citations to the classifier | getCitations getCitations,ClassifierParameters-method |
| Obtain classifier classifications. | getClassifications getClassifications,ClassifierResults-method |
| Obtain a classifier definition. | getClassifier getClassifier,character-method getClassifier,ClassifierResults-method |
| Obtain the decision boundaries defined for the classifier. | getDecisionBoundaries getDecisionBoundaries,ClassifierParameters-method |
| Obtain classifiers' description. | getDescription getDescription,ClassifierParameters-method |
| Obtain classifiers' event chain. | getEventChain getEventChain,ClassifierParameters-method |
| Obtain classifiers' intercept. | getIntercept getIntercept,ClassifierParameters-method |
| Obtain classifiers' reference means. | getMeans getMeans,ClassifierParameters-method |
| Obtain object names. | getName getName,ClassifierParameters-method getName,ClassifierResults-method getName,TransformationProcess-method |
| Obtain normalization method | getNormalizationMethod getNormalizationMethod,ClassifierParameters-method getNormalizationMethod,FixedExpressionData-method getNormalizationMethods |
| Obtain probe-set names. | getProbeNames getProbeNames,ClassifierParameters-method |
| Obtain classifier score. | getScores getScores,ClassifierResults-method |
| Obtain classifiers' reference standard deviations. | getSds getSds,ClassifierParameters-method |
| Obtain the targetValue | getTargetValue getTargetValue,FixedExpressionData-method |
| Obtain classifier training data. | getTrainingData getTrainingData,ClassifierParameters-method |
| Obtain the weighting type used to obtain a classifier result. | getWeightingType getWeightingType,ClassifierResults-method getWeightingTypes |
| Obtain classifier weights. | getWeights getWeights,ClassifierParameters-method |
| Perform classification. | runClassifier runClassifier,character,FixedExpressionData-method runClassifier,ClassifierParameters,FixedExpressionData-method runClassifier,ClassifierResults,FixedExpressionData-method |
| Prepare data. | setNormalizationMethod |
| Show classifier names and descriptions. | showClassifierList |