# Classes and methods for performing benchmark comparisons

## Documentation for package ‘SummarizedBenchmark’ version 2.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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