Package index

All functions

bpPlot()

Customized boxplot visualization of benchmark results

cacheResource()

Caching of a resource

evalNrSigSets() evalNrSets()

Evaluating gene set rankings for the number of (significant) sets

evalRandomGS()

Evaluation of enrichment methods on random gene sets

evalRelevance() compOpt() compRand()

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

readDataId2diseaseCodeMap()

Read a mapping between dataset ID and disease code

readResults()

Reading results of enrichment analysis

runDE() metaFC() writeDE() plotDEDistribution() plotNrSamples()

Differential expression analysis for datasets of a compendium

runEA()

Application of enrichment methods to multiple datasets