# Generated by roxygen2: do not edit by hand

S3method(FitOptions, data.frame)
S3method(FitOptions, default)
S3method(summary, GSEAparams)

S3method(summary, IGSAinput)

S3method(summary, MIGSAres)

S3method(summary, SEAparams)

export(FitOptions)
export(FitOptions.data.frame)
export(FitOptions.default)
export(GSEAparams)
export(IGSAinput)
export(SEAparams)
export(summary.GSEAparams)
export(summary.IGSAinput)
export(summary.MIGSAres)
export(summary.SEAparams)
exportClasses(ExprData)
exportClasses(FitOptions)
exportClasses(MIGSAres)
exportMethods("$")
exportMethods("[")
exportMethods("exprData<-")
exportMethods("fitOptions<-")
exportMethods("geneSetsList<-")
exportMethods("gseaParams<-")
exportMethods("name<-")
exportMethods("seaParams<-")
exportMethods(MIGSA)
exportMethods(MIGSAmGSZ)
exportMethods(as.Genesets)
exportMethods(as.data.frame)
exportMethods(colnames)
exportMethods(dim)
exportMethods(downloadEnrichrGeneSets)
exportMethods(enrichrGeneSets)
exportMethods(exprData)
exportMethods(filterByGenes)
exportMethods(fitOptions)
exportMethods(geneSetBarplot)
exportMethods(geneSetsFromFile)
exportMethods(geneSetsList)
exportMethods(genesBarplot)
exportMethods(genesHeatmap)
exportMethods(genesInSets)
exportMethods(getAdditionalInfo)
exportMethods(getDEGenes)
exportMethods(getHeights)
exportMethods(goTree)
exportMethods(gseaParams)
exportMethods(head)
exportMethods(loadGo)
exportMethods(merge)
exportMethods(migsaGoTree)
exportMethods(migsaHeatmap)
exportMethods(name)
exportMethods(seaParams)
exportMethods(setEnrCutoff)
exportMethods(show)
exportMethods(tail)
import(BiocGenerics)
import(methods)
importClassesFrom(GSEABase,GOCollection)
importClassesFrom(GSEABase,GeneSetCollection)
importClassesFrom(edgeR,DGEList)
importClassesFrom(graph,graphNEL)
importClassesFrom(limma,MAList)
importFrom(AnnotationDbi,Ontology)
importFrom(AnnotationDbi,Term)
importFrom(AnnotationDbi,as.list)
importFrom(AnnotationDbi,mappedkeys)
importFrom(Biobase,testBioCConnection)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpparam)
importFrom(GO.db,GOBPPARENTS)
importFrom(GO.db,GOCCPARENTS)
importFrom(GO.db,GOMFPARENTS)
importFrom(GO.db,GOTERM)
importFrom(GOstats,GOGraph)
importFrom(GSEABase,"geneIds<-")
importFrom(GSEABase,"setIdentifier<-")
importFrom(GSEABase,"setName<-")
importFrom(GSEABase,EntrezIdentifier)
importFrom(GSEABase,GOCollection)
importFrom(GSEABase,GeneSet)
importFrom(GSEABase,GeneSetCollection)
importFrom(GSEABase,NullCollection)
importFrom(GSEABase,collectionType)
importFrom(GSEABase,geneIds)
importFrom(GSEABase,setIdentifier)
importFrom(GSEABase,setName)
importFrom(RBGL,isomorphism)
importFrom(RJSONIO,fromJSON)
importFrom(Rgraphviz,'nodeData<-')
importFrom(Rgraphviz,'nodeDataDefaults<-')
importFrom(Rgraphviz,layoutGraph)
importFrom(Rgraphviz,nodeData)
importFrom(Rgraphviz,renderGraph)
importFrom(compiler,cmpfun)
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,setkey)
importFrom(edgeR,"[.DGEList")
importFrom(edgeR,DGEList)
importFrom(futile.logger,flog.debug)
importFrom(futile.logger,flog.error)
importFrom(futile.logger,flog.info)
importFrom(futile.logger,flog.warn)
importFrom(ggdendro,ggdendrogram)
importFrom(ggplot2,aes)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,theme)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(grDevices,col2rgb)
importFrom(grDevices,hcl)
importFrom(grDevices,rgb)
importFrom(graph,'edgeRenderInfo<-')
importFrom(graph,'graphRenderInfo<-')
importFrom(graph,'nodeRenderInfo<-')
importFrom(graph,addEdge)
importFrom(graph,degree)
importFrom(graph,edges)
importFrom(graph,nodes)
importFrom(graph,removeNode)
importFrom(graphics,legend)
importFrom(grid,grid.layout)
importFrom(grid,grid.newpage)
importFrom(grid,pushViewport)
importFrom(grid,viewport)
importFrom(ismev,gum.fit)
importFrom(limma,contrasts.fit)
importFrom(limma,lmFit)
importFrom(limma,treat)
importFrom(limma,voom)
importFrom(matrixStats,colSds)
importFrom(matrixStats,colVars)
importFrom(matrixStats,rowMedians)
importFrom(org.Hs.eg.db,org.Hs.egALIAS2EG)
importFrom(org.Hs.eg.db,org.Hs.egGO2ALLEGS)
importFrom(reshape2,melt)
importFrom(stats,as.dendrogram)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pbinom)
importFrom(stats,phyper)
importFrom(utils,combn)
importFrom(vegan,vegdist)
