| 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')