setFeatureSelectionOptions-methods: getFeatureSelectionOptions<- Method to modify the attributes...

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

Description

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.

Arguments

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.

Value

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" numericSlot 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.

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
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')

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