Classes and methods for performing benchmark comparisons


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Documentation for package ‘SummarizedBenchmark’ version 2.2.3

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addMethod Add new method to BenchDesign object
addPerformanceMetric Add a performance metric definition to a 'SummarizedBenchmark' object.
allSB SummarizedBenchmark object of isoform quantification results
allSB,quantSB SummarizedBenchmark object of isoform quantification results
assayNames Accessor and replacement functions for the slots of a SummarizedBenchmark object.
assayNames-method Accessor and replacement functions for the slots of a SummarizedBenchmark object.
assayNames<--method Accessor and replacement functions for the slots of a SummarizedBenchmark object.
availableMetrics availableMetrics
BDData Create a new BDData
BDData-class BDMethod class
BDData-method Create a new BDData
BDData<- BenchDesign Accessors
BDData<--method BenchDesign Accessors
BDMethod Create a new BDMethod
BDMethod-class BDMethod class
BDMethod-method Create a new BDMethod
BDMethod-method BDMethodList Accessors
BDMethod-method BenchDesign Accessors
BDMethod<- BenchDesign Accessors
BDMethod<--method BDMethodList Accessors
BDMethod<--method BenchDesign Accessors
BDMethodList Create a new BDMethodList
BDMethodList-accessors BDMethodList Accessors
BDMethodList-class BDMethodList class
BDMethodList-method Create a new BDMethodList
BDMethodList-method BenchDesign Accessors
BDMethodList-method Accessor and replacement functions for the slots of a SummarizedBenchmark object.
BDMethodList<- BenchDesign Accessors
BDMethodList<--method BenchDesign Accessors
BenchDesign Create a new BenchDesign
BenchDesign-accessors BenchDesign Accessors
BenchDesign-class BenchDesign class
BenchDesign-method Create a new BenchDesign
BenchDesign-method Accessor and replacement functions for the slots of a SummarizedBenchmark object.
buildBench Make SummarizedBenchmark from BenchDesign
coerce Create a new BDMethodList
compareBDData Compare BDData objects
compareBDMethod Compare BDMethod objects
compareBenchDesigns Compare BenchDesign objects
compareBenchDesigns-method Compare BenchDesign objects
dropMethod Remove method from BenchDesign object
estimateMetricsForAssay Estimate performance metrics.
estimatePerformanceMetrics Estimate performance metrics.
expandMethod Expand method in BenchDesign object across parameter settings
groundTruths Accessor and replacement functions for the slots of a SummarizedBenchmark object.
groundTruths-method Accessor and replacement functions for the slots of a SummarizedBenchmark object.
groundTruths<- Accessor and replacement functions for the slots of a SummarizedBenchmark object.
groundTruths<--method Accessor and replacement functions for the slots of a SummarizedBenchmark object.
hashBDData Convert BDData to BDData with MD5 Hash
hashBDData-method Convert BDData to BDData with MD5 Hash
mcols<--method Accessor and replacement functions for the slots of a SummarizedBenchmark object.
modifyMethod Modify definition of method in BenchDesign object
performanceMetrics Accessor and replacement functions for the slot 'performanceMetrics' of a SummarizedBenchmark object.
performanceMetrics-method Accessor and replacement functions for the slot 'performanceMetrics' of a SummarizedBenchmark object.
performanceMetrics<- Accessor and replacement functions for the slot 'performanceMetrics' of a SummarizedBenchmark object.
performanceMetrics<--method Accessor and replacement functions for the slot 'performanceMetrics' of a SummarizedBenchmark object.
plotMethodsOverlap Calls UpSetR for qvalues of a 'SummarizedBenchmark' object.
plotROC Plotting ROC curves
printMethod Pretty print methods in a BenchDesign
printMethods Pretty print methods in a BenchDesign
sb SummarizedBenchmark example
show-method BDMethod class
show-method BDMethod class
show-method BDMethodList class
show-method BenchDesign class
SummarizedBenchmark Constructor function for SummarizedBenchmark objects.
SummarizedBenchmark-accessors Accessor and replacement functions for the slots of a SummarizedBenchmark object.
SummarizedBenchmark-class SummarizedBenchmark class documentation
tdat Example data.frame containing results for 50 two-sample t-tests.
tidyBDMethod Tidy BDMethod Data
tidyBDMethod-method Tidy BDMethod Data
tidyUpMetrics Reformat performance metrics to a long format.
truthdat SummarizedBenchmark example
txi SummarizedBenchmark example
updateBench Update SummarizedBenchmark object