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| 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 |