getFeatureSelectionOptions-methods: getFeatureSelectionOptions Method to access the attributes of...

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

Description

This method provides an easy interface to access the attributes of the object of class featureSelectionOptions related to a particular assessment, directly from this object assessment. The argument topic specifies which part of the featureSelectionOptions is of interest.

Arguments

object

Object of class assessment. Object assessment of interest

topic

character. Optional argument that specifies which attribute of the featureSelectionOptions is requested, the possible values are: "optionValues" (Access the slot optionValues of the featureSelectionOptions), "noOfOptions" (Access the slot noOfOptions of the featureSelectionOptions), if the featureSelectionOptions object is an object of class geneSubsets, then the following values are also available for the argument topic "subsetsSizes" (Access the slot optionValues of the geneSubsets), "noModels" (Access the slot noOfOptions of the geneSubsets), "maxSubsetSize" (Access the slot maxSelectedFeatures of the geneSubsets), "speed" (Access the slot speed of the featureSelectionOptions), if the featureSelectionOptions object is an object of class thresholds, then the following values are also available for the argument topic "thresholds" (Access the slot optionValues of the object thresholds), "noThresholds" (Access the slot noOfOptions of the object thresholds) if the topic is missing then the whole featureSelectionOptions object is returned.

Value

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

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

If topic is "optionValues" numeric corresponding to the optionValues of the featureSelectionOptions

If topic is "noOfOptions" numeric corresponding to the noOfOptions of the featureSelectionOptions

If object is of class geneSubsets and topic is "maxSubsetSize" numeric corresponding to the maxSubsetSize of the geneSubsets

If object is of class geneSubsets and topic is "subsetsSizes" numeric corresponding to the optionValues of the geneSubsets

If object is of class geneSubsets and topic is "noModels" numeric corresponding to the noOfOptions of the geneSubsets

If object is of class geneSubsets and topic is "speed" numeric corresponding to the speed of the geneSubsets

If object is of class thresholds and topic is "thresholds" numeric corresponding to the optionValues of the object of class thresholds

If object is of class thresholds and topic is "noThresholds" numeric corresponding to the noOfOptions of the object of class thresholds

Methods

object = "assessment"

The method is only applicable on objects of class assessment.

Author(s)

Camille Maumet

See Also

featureSelectionOptions, assessment

Examples

# With an assessment using RFE
#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')

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

# Return the whole object 'featureSelectionOptions' (an object of class geneSusbsets)
getFeatureSelectionOptions(myExpe)
# Size of the biggest subset
getFeatureSelectionOptions(myExpe, topic='maxSubsetSize')
# All sizes of subsets
getFeatureSelectionOptions(myExpe, topic='subsetsSizes')
# Speed
getFeatureSelectionOptions(myExpe, topic='speed')
# Number of subsets
getFeatureSelectionOptions(myExpe, topic='noModels') == getNoModels(mySubsets)

# With an assessment using NSC as a feature selection method
myThresholds <- new("thresholds", optionValues=c(0.1,0.2,0.3))
myExpe2 <- new("assessment", dataset=vV70genes,
                                   noFolds1stLayer=10,
                                   noFolds2ndLayer=9,
                                   classifierName="nsc",
                                   featureSelectionMethod='nsc',
                                   typeFoldCreation="original",
                                   svmKernel="linear",
                                   noOfRepeat=2,
                                   featureSelectionOptions=myThresholds)

# Return the whole object 'featureSelectionOptions' (an object of class geneSusbsets)
getFeatureSelectionOptions(myExpe2)
# vector of thresholds
getFeatureSelectionOptions(myExpe2, topic='thresholds')
# Number of thresholds
getFeatureSelectionOptions(myExpe2, topic='noThresholds')

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