BDData                  Create a new BDData object
BDData-class            BDData class
BDData<-                Set data in BenchDesign object
BDMethod                Create a new BDMethod object
BDMethod-class          BDMethod class
BDMethod<-              Set method in list or BenchDesign object
BDMethodList            Create a new BDMethodList object
BDMethodList-class      BDMethodList class
BDMethodList<-          Set method list in BenchDesign object
BenchDesign             Create a new BenchDesign object
BenchDesign-class       BenchDesign class
SummarizedBenchmark     Create a new SummarizedBenchmark object
SummarizedBenchmark-class
                        SummarizedBenchmark class
addMethod               Add method to BenchDesign object
addPerformanceMetric    Add performance metric to SummarizedBenchmark
                        object
allSB                   SummarizedBenchmark object of isoform
                        quantification results
assayNames<-,SummarizedBenchmark,character-method
                        Set assay names in SummarizedBenchmark object
availableMetrics        List pre-defined metrics for
                        SummarizedBenchmark objects
buildBench              Execute BenchDesign
compareBDData           Compare BDData objects
compareBDMethod         Compare BDMethod objects
compareBenchDesigns     Compare BenchDesign objects
dropMethod              Remove method from BenchDesign object
estimateMetricsForAssay
                        Estimate performance metrics in
                        SummarizedBenchmark object
expandMethod            Expand method in BenchDesign object
groundTruths            Get ground truths in SummarizedBenchmark object
groundTruths<-          Set ground truths in SummarizedBenchmark object
hashBDData              Hash data in BDData object
mcols<-,SummarizedBenchmark-method
                        Set meta data columns in SummarizedBenchmark
                        object
modifyMethod            Modify method in BenchDesign object
performanceMetrics      Get performance metrics in SummarizedBenchmark
                        object
performanceMetrics<-    Set performance metrics in SummarizedBenchmark
                        object
plotMethodsOverlap      Plot UpSetR for SummarizedBenchmark object
plotROC                 Plot ROC curve for SummarizedBenchmark object
printMethod             Pretty print methods in a BenchDesign object
sb                      SummarizedBenchmark example
show,BDData-method      Show BDData object
show,BDMethod-method    Show BDMethod object
show,BDMethodList-method
                        Show BDMethodList object
show,BenchDesign-method
                        Show BenchDesign object
tdat                    Example data.frame containing results for 50
                        two-sample t-tests.
tidyBDMethod            Tidy BDMethod Data
tidyUpMetrics           Tidy up performance metrics in
                        SummarizedBenchmark object
updateBench             Check/Update SummarizedBenchmark
