Package: SummarizedBenchmark 2.23.0

Patrick Kimes

SummarizedBenchmark: Classes and methods for performing benchmark comparisons

This package defines the BenchDesign and SummarizedBenchmark classes for building, executing, and evaluating benchmark experiments of computational methods. The SummarizedBenchmark class extends the RangedSummarizedExperiment object, and is designed to provide infrastructure to store and compare the results of applying different methods to a shared data set. This class provides an integrated interface to store metadata such as method parameters and software versions as well as ground truths (when these are available) and evaluation metrics.

Authors:Alejandro Reyes [aut], Patrick Kimes [aut, cre]

# Install 'SummarizedBenchmark' in R:

install.packages('SummarizedBenchmark', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/areyesq89/summarizedbenchmark/issues

Datasets:

allSB - SummarizedBenchmark object of isoform quantification results
sb - SummarizedBenchmark example
tdat - Example data.frame containing results for 50 two-sample t-tests.
truthdat - SummarizedBenchmark example
txi - SummarizedBenchmark example

On BioConductor:SummarizedBenchmark-2.23.0(bioc 3.20)SummarizedBenchmark-2.22.0(bioc 3.19)

bioconductor-package

34 exports 1.58 score 76 dependencies 3 mentions

Last updated 2 months agofrom:8c13099f25

Exports:addMethod addPerformanceMetric assayNames<-availableMetrics BDData BDData<-BDMethod BDMethod<-BDMethodList BDMethodList<-BenchDesign buildBench compareBDData compareBDMethod compareBenchDesigns dropMethod estimateMetricsForAssay estimatePerformanceMetrics expandMethod groundTruths groundTruths<-hashBDData mcols<-modifyMethod performanceMetrics performanceMetrics<-plotMethodsOverlap plotROC printMethod printMethods SummarizedBenchmark tidyBDMethod tidyUpMetrics updateBench

Dependencies:abind askpass BH Biobase BiocGenerics BiocParallel cli codetools colorspace cpp11 crayon curl DelayedArray digest dplyr fansi farver formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gridExtra gtable httr IRanges isoband jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mclust mgcv mime munsell nlme openssl pillar pkgconfig plyr purrr R6 RColorBrewer Rcpp rlang S4Arrays S4Vectors scales sessioninfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils UpSetR utf8 vctrs viridisLite withr XVector zlibbioc

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Help page	Topics
Add method to BenchDesign object	addMethod
Add performance metric to SummarizedBenchmark object	addPerformanceMetric
SummarizedBenchmark object of isoform quantification results	allSB allSB,quantSB
Set assay names in SummarizedBenchmark object	assayNames<-,SummarizedBenchmark,character-method
List pre-defined metrics for SummarizedBenchmark objects	availableMetrics
Create a new BDData object	BDData BDData,ANY-method BDData,BDData-method BDData,BenchDesign-method BDData,SummarizedBenchmark-method
BDData class	BDData-class
Set data in BenchDesign object	BDData<- BDData<-,BenchDesign,BDDataOrNULL-method
Create a new BDMethod object	BDMethod BDMethod,BDMethodList-method BDMethod,BenchDesign-method BDMethod,function-method BDMethod,quosure-method
BDMethod class	BDMethod-class
Set method in list or BenchDesign object	BDMethod<- BDMethod<-,BDMethodList,character,BDMethod-method BDMethod<-,BDMethodList,character,NULL-method BDMethod<-,BenchDesign,character,BDMethod-method BDMethod<-,BenchDesign,character,NULL-method
Create a new BDMethodList object	BDMethodList BDMethodList,ANY-method BDMethodList,BenchDesign-method BDMethodList,SummarizedBenchmark-method coerce
BDMethodList class	BDMethodList-class
Set method list in BenchDesign object	BDMethodList<- BDMethodList<-,BenchDesign,BDMethodList-method
Create a new BenchDesign object	BenchDesign BenchDesign,ANY-method BenchDesign,SummarizedBenchmark-method
BenchDesign class	BenchDesign-class
Execute BenchDesign	buildBench
Compare BDData objects	compareBDData
Compare BDMethod objects	compareBDMethod
Compare BenchDesign objects	compareBenchDesigns compareBenchDesigns,BenchDesign,BenchDesign-method compareBenchDesigns,BenchDesign,SummarizedBenchmark-method compareBenchDesigns,SummarizedBenchmark,BenchDesign-method compareBenchDesigns,SummarizedBenchmark,missing-method compareBenchDesigns,SummarizedBenchmark,SummarizedBenchmark-method
Remove method from BenchDesign object	dropMethod
Estimate performance metrics in SummarizedBenchmark object	estimateMetricsForAssay estimatePerformanceMetrics
Expand method in BenchDesign object	expandMethod
Get ground truths in SummarizedBenchmark object	groundTruths groundTruths,SummarizedBenchmark-method
Set ground truths in SummarizedBenchmark object	groundTruths<- groundTruths<-,SummarizedBenchmark-method
Hash data in BDData object	hashBDData hashBDData,BDData-method hashBDData,BenchDesign-method
Set meta data columns in SummarizedBenchmark object	mcols<-,SummarizedBenchmark-method
Modify method in BenchDesign object	modifyMethod
Get performance metrics in SummarizedBenchmark object	performanceMetrics performanceMetrics,SummarizedBenchmark-method
Set performance metrics in SummarizedBenchmark object	performanceMetrics<- performanceMetrics<-,SummarizedBenchmark,SimpleList-method
Plot UpSetR for SummarizedBenchmark object	plotMethodsOverlap
Plot ROC curve for SummarizedBenchmark object	plotROC
Pretty print methods in a BenchDesign object	printMethod printMethods
SummarizedBenchmark example	sb truthdat txi
Show BDData object	show,BDData-method
Show BDMethod object	show,BDMethod-method
Show BDMethodList object	show,BDMethodList-method
Show BenchDesign object	show,BenchDesign-method
Create a new SummarizedBenchmark object	SummarizedBenchmark
SummarizedBenchmark class	SummarizedBenchmark-class
Example data.frame containing results for 50 two-sample t-tests.	tdat
Tidy BDMethod Data	tidyBDMethod tidyBDMethod,BDMethod-method tidyBDMethod,BenchDesign-method tidyBDMethod,list-method tidyBDMethod,SimpleList-method
Tidy up performance metrics in SummarizedBenchmark object	tidyUpMetrics
Check/Update SummarizedBenchmark	updateBench

Package: SummarizedBenchmark 2.23.0

SummarizedBenchmark: Classes and methods for performing benchmark comparisons

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