import("Rcpp")
importClassFrom("Biobase", "eSet")
importFrom("Biobase", "fData", "featureNames", "exprs")
importFrom("utils", "head")
importFrom("methods", "is", "new")
importFrom("stats", "pt", "wilcox.test")

exportClass(GmtList, SignedGenesets, IndexList, SignedIndexList)
export(GmtList, SignedGenesets, IndexList, SignedIndexList, as.gmtlist)
export(matchGenes)

export(offset, "offset<-")

## GMT functions
export(readGmt,
       gmtlist2signedGenesets,
       readSignedGmt)

## helper functions
export(entropy,
       entropyDiversity,
       entropySpecificity,
       sampleSpecialization)
export(gini)
export(absLog10p)
export(filterPmat)
export(simplifyMatrix)
export(valTypes)

export(wmwTestInR)
export(wmwTest)

useDynLib(BioQC, .registration=TRUE, .fixes="C_")
