BDData                  Create a new BDData
BDData-class            BDMethod class
BDMethod                Create a new BDMethod
BDMethod-class          BDMethod class
BDMethodList            Create a new BDMethodList
BDMethodList-accessors
                        BDMethodList Accessors
BDMethodList-class      BDMethodList class
BenchDesign             Create a new BenchDesign
BenchDesign-accessors   BenchDesign Accessors
BenchDesign-class       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
addMethod               Add new method to BenchDesign object
addPerformanceMetric    Add a performance metric definition to a
                        'SummarizedBenchmark' object.
allSB                   SummarizedBenchmark object of isoform
                        quantification results
availableMetrics        availableMetrics
buildBench              Make SummarizedBenchmark from BenchDesign
compareBDData           Compare BDData objects
compareBDMethod         Compare BDMethod objects
compareBenchDesigns     Compare BenchDesign objects
dropMethod              Remove method from BenchDesign object
estimateMetricsForAssay
                        Estimate performance metrics.
expandMethod            Expand method in BenchDesign object across
                        parameter settings
hashBDData              Convert BDData to BDData with MD5 Hash
modifyMethod            Modify definition of method in BenchDesign
                        object
performanceMetrics      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
sb                      SummarizedBenchmark example
tdat                    Example data.frame containing results for 50
                        two-sample t-tests.
tidyBDMethod            Tidy BDMethod Data
tidyUpMetrics           Reformat performance metrics to a long format.
updateBench             Update SummarizedBenchmark object
