Reproducible GSEA Benchmarking

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Documentation for package ‘GSEABenchmarkeR’ version 1.29.1

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

Help Pages

bpPlot	Customized boxplot visualization of benchmark results
cacheResource	Caching of a resource
compOpt	Evaluating phenotype relevance of gene set rankings
compRand	Evaluating phenotype relevance of gene set rankings
evalNrSets	Evaluating gene set rankings for the number of (significant) sets
evalNrSigSets	Evaluating gene set rankings for the number of (significant) sets
evalRandomGS	Evaluation of enrichment methods on random gene sets
evalRelevance	Evaluating phenotype relevance of gene set rankings
evalTypeIError	Evaluation of the type I error rate of enrichment methods
loadEData	Loading pre-defined and user-defined expression data
maPreproc	Preprocessing of microarray expression data
metaFC	Differential expression analysis for datasets of a compendium
plotDEDistribution	Differential expression analysis for datasets of a compendium
plotNrSamples	Differential expression analysis for datasets of a compendium
readDataId2diseaseCodeMap	Read a mapping between dataset ID and disease code
readResults	Reading results of enrichment analysis
runDE	Differential expression analysis for datasets of a compendium
runEA	Application of enrichment methods to multiple datasets
writeDE	Differential expression analysis for datasets of a compendium