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 |