Classes and methods for performing benchmark comparisons

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Documentation for package ‘SummarizedBenchmark’ version 2.5.0

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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