Package: geneClassifiers 1.29.0

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:R Kuiper [cre, aut]

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geneClassifiers.pdf |geneClassifiers.html✨
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

Datasets:

exampleMAS5 - Example MAS5.0 ExpressionSet

On BioConductor:geneClassifiers-1.29.0(bioc 3.20)geneClassifiers-1.28.0(bioc 3.19)

bioconductor-package

23 exports 0.71 score 2 dependencies

Last updated 2 months agofrom:6ccbc07c45

Exports:getBatchCorrection getCitations getClassifications getClassifier getDecisionBoundaries getDescription getEventChain getIntercept getMeans getName getNormalizationMethod getNormalizationMethods getProbeNames getScores getSds getTargetValue getTrainingData getWeightingType getWeightingTypes getWeights runClassifier setNormalizationMethod showClassifierList

Dependencies:Biobase BiocGenerics

geneClassifiers and missing probesets

Rendered fromMissingCovariates.Rnwusingutils::Sweaveon Jun 30 2024.

Last update: 2016-12-21
Started: 2016-10-03

geneClassifiers introduction

Rendered fromgeneClassifiers.Rnwusingutils::Sweaveon Jun 30 2024.

Last update: 2016-12-21
Started: 2016-10-03

Citation

Development and contributors

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