setFeatureSelectionOptions-methods {Rmagpie} | R Documentation |
This method provides an easy interface to modify 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.
This method is only available none of the one-layer
CV or two-layers CV have been performed and the final classifier has not been determined yet.
object |
Object of class assessment . Object assessment of interest |
topic |
character . Optional argument that specifies which attribute of
the featureSelectionOptions must be replaced, the possible values are:
"optionValues" (slot optionValues of the featureSelectionOptions),
"noOfOptions" (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" (slot optionValues of the geneSubsets),
"noModels" (slot noOfOptions of the geneSubsets),
"maxSubsetSize" (slot maxSelectedFeatures of the geneSubsets),
"speed" (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" (slot optionValues of the object thresholds),
"noThresholds" (slot noOfOptions of the object thresholds)
if the topic is missing then the whole featureSelectionOptions object is replaced. |
The methods modifies the object of class assessment and returned the slot modified
accordingly to the request provided by topic
.
If topic
is missing
object of class featureSelectionOptions
featureSelectionOptions corresponding to the assessment is replaced by value
.
If topic
is "optionValues"
numeric
Slot optionValues
of the featureSelectionOptions is replaced by value
.
If topic
is "noOfOptions"
numeric
Slot noOfOptions
of the featureSelectionOptions is replaced by value
.
If object
is of class geneSubsets
and topic
is "maxSubsetSize"
numeric
Slot maxSubsetSize
of the geneSubsets is replaced by value
.
If object
is of class geneSubsets
and topic
is "subsetsSizes"
numeric
Slot optionValues
of the geneSubsets is replaced by value
.
If object
is of class geneSubsets
and topic
is "noModels"
numeric
Slot noOfOptions
of the geneSubsets is replaced by value
.
If object
is of class geneSubsets
and topic
is "speed"
numeric
Slot speed
of the geneSubsets is replaced by value
.
If object
is of class thresholds
and topic
is "thresholds"
numeric
Slot optionValues
of the object of class thresholds is replaced by value
.
If object
is of class thresholds
and topic
is "noThresholds"
numeric
Slot noOfOptions
of the object of class thresholds is replaced by value
.
Camille Maumet
featureSelectionOptions
, assessment
# With an assessment using RFE 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) # Modify the size of the biggest subset getFeatureSelectionOptions(myExpe, topic='maxSubsetSize') <- 70 getFeatureSelectionOptions(myExpe, topic='maxSubsetSize') # Modify all the sizes of subsets getFeatureSelectionOptions(myExpe, topic='subsetsSizes') <- c(1,5,10,25,30) getFeatureSelectionOptions(myExpe, topic='subsetsSizes') # Modify the speed getFeatureSelectionOptions(myExpe, topic='speed') <- 'slow' getFeatureSelectionOptions(myExpe, topic='speed') # Modify the entire geneSubsets getFeatureSelectionOptions(myExpe) <- mySubsets getFeatureSelectionOptions(myExpe, topic='maxSubsetSize') getFeatureSelectionOptions(myExpe, topic='subsetsSizes') getFeatureSelectionOptions(myExpe, topic='speed') getFeatureSelectionOptions(myExpe, topic='noModels') # 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) otherThresholds <- new("thresholds", optionValues=c(0,0.5,1,1.5,2,2.5,3)) # Modify the whole object 'featureSelectionOptions' (an object of class thresholds) getFeatureSelectionOptions(myExpe2) <- otherThresholds getFeatureSelectionOptions(myExpe2, topic='thresholds') getFeatureSelectionOptions(myExpe2, topic='noThresholds')