# Classes and methods for performing benchmark comparisons

## Documentation for package ‘SummarizedBenchmark’ version 2.5.0

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

## Help Pages

addMethod | Add method to BenchDesign object
addPerformanceMetric | Add performance metric to SummarizedBenchmark object
allSB | SummarizedBenchmark object of isoform quantification results
allSB,quantSB | SummarizedBenchmark object of isoform quantification results
assayNames<--method | Set assay names in SummarizedBenchmark object
availableMetrics | List pre-defined metrics for SummarizedBenchmark objects
BDData | Create a new BDData object
BDData-class | BDData class
BDData-method | Create a new BDData object
BDData<- | Set data in BenchDesign object
BDData<--method | Set data in BenchDesign object
BDMethod | Create a new BDMethod object
BDMethod-class | BDMethod class
BDMethod-method | Create a new BDMethod object
BDMethod<- | Set method in list or BenchDesign object
BDMethod<--method | Set method in list or BenchDesign object
BDMethodList | Create a new BDMethodList object
BDMethodList-class | BDMethodList class
BDMethodList-method | Create a new BDMethodList object
BDMethodList<- | Set method list in BenchDesign object
BDMethodList<--method | Set method list in BenchDesign object
BenchDesign | Create a new BenchDesign object
BenchDesign-class | BenchDesign class
BenchDesign-method | Create a new BenchDesign object
buildBench | Execute BenchDesign
coerce | Create a new BDMethodList object
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 in SummarizedBenchmark object
estimatePerformanceMetrics | Estimate performance metrics in SummarizedBenchmark object
expandMethod | Expand method in BenchDesign object
groundTruths | Get ground truths in SummarizedBenchmark object
groundTruths-method | Get ground truths in SummarizedBenchmark object
groundTruths<- | Set ground truths in SummarizedBenchmark object
groundTruths<--method | Set ground truths in SummarizedBenchmark object
hashBDData | Hash data in BDData object
hashBDData-method | Hash data in BDData object
mcols<--method | Set meta data columns in SummarizedBenchmark object
modifyMethod | Modify method in BenchDesign object
performanceMetrics | Get performance metrics in SummarizedBenchmark object
performanceMetrics-method | Get performance metrics in SummarizedBenchmark object
performanceMetrics<- | Set performance metrics in SummarizedBenchmark object
performanceMetrics<--method | 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
printMethods | Pretty print methods in a BenchDesign object
sb | SummarizedBenchmark example
show-method | Show BDData object
show-method | Show BDMethod object
show-method | Show BDMethodList object
show-method | Show BenchDesign object
SummarizedBenchmark | Create a new SummarizedBenchmark object
SummarizedBenchmark-class | SummarizedBenchmark class
tdat | Example data.frame containing results for 50 two-sample t-tests.
tidyBDMethod | Tidy BDMethod Data
tidyBDMethod-method | Tidy BDMethod Data
tidyUpMetrics | Tidy up performance metrics in SummarizedBenchmark object
truthdat | SummarizedBenchmark example
txi | SummarizedBenchmark example
updateBench | Check/Update SummarizedBenchmark