getDataset-methods: getDataset Method to access the attributes of a dataset from...

In Rmagpie: MicroArray Gene-expression-based Program In Error rate estimation

Description

This method provides an easy interface to access the attributes of a dataset directly from an object assessment. The argument topic specifies which part of the dataset is of interest.

Arguments

object	Object of class assessment. Object assessment of interest
topic	character. Optional argument that specifies which attribute of the dataset is requested, the possible values are "dataId" (slot dataId of the dataset), "dataPath" (slot dataPath of the dataset), "geneExprFile" (slot geneExprFile of the dataset), "classesFile" (slot classesFile of the dataset), "eset" (slot eset of the dataset) if the "topic" is missing then the whole dataset object is returned.

Value

The value returned by the method changes accordingly to the "topic" argument.

If "topic" is missing object of class dataset the dataset corresponding to the assessment of interest

If "topic" is "dataId" object of class character corresponding to the dataId of the dataset

If "topic" is "dataPath" object of class character corresponding to the dataPath of the dataset

If "topic" is "geneExprFile" object of class character corresponding to the geneExprFile of the dataset

If "topic" is "classesFile" object of class character corresponding to the classesFile of the dataset

If "topic" is "eset" object of class ExpressionSetOrNull corresponding to the eset of the dataset

Methods

object = "assessment"

The method is only applicable on objects of class assessment.

Author(s)

Camille Maumet

See Also

assessment

Examples

#dataPath <- file.path("C:", "Documents and Settings", "c.maumet", "My Documents", "Programmation", "Sources", "SVN", "R package", "data")
#aDataset <- new("dataset", dataId="vantVeer_70", dataPath=dataPath)
#aDataset <- loadData(aDataset)

data('vV70genesDataset')

expeOfInterest <- new("assessment", dataset=vV70genes,
                                   noFolds1stLayer=10,
                                   noFolds2ndLayer=9,
                                   classifierName="svm",
                                   typeFoldCreation="original",
                                   svmKernel="linear",
                                   noOfRepeat=2,
                                   featureSelectionOptions=new("geneSubsets", optionValues=c(1,2,3,4,5,6)))

getDataset(expeOfInterest)

Rmagpie documentation built on Nov. 8, 2020, 11:09 p.m.