getFeatureSelectionOptions-methods {Rmagpie} | R Documentation |
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.
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. |
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
Camille Maumet
featureSelectionOptions
, assessment
# 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')