# Classes and methods for performing benchmark comparisons

## Documentation for package ‘SummarizedBenchmark’ version 1.0.4

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

## Help Pages

Accessors | Accessor and replacement functions for the slots of a SummarizedBenchmark object.
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
BenchDesign | Create a new BenchDesign
buildBench | Make SummarizedBenchmark from BenchDesign
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.
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
SummarizedBenchmark | Constructor function for SummarizedBenchmark objects.
SummarizedBenchmark-class | SummarizedBenchmark class documentation
tdat | Example data.frame containing results for 50 two-sample t-tests.
tidyUpMetrics | Reformat performance metrics to a long format.
truthdat | SummarizedBenchmark example
txi | SummarizedBenchmark example