# Generated by roxygen2: do not edit by hand

S3method(degtable,topResult)
S3method(print,topResult)
S3method(res,topResult)
S3method(topo.sig,topResult)
export(CePa)
export(DEGraph)
export(PRS_wrapper)
export(PWEA)
export(SPIA)
export(TAPPA)
export(TopologyGSA)
export(clipper)
export(convertIdentifiersByVector)
export(degtable)
export(prs)
export(prsWeights)
export(res)
export(topo.sig)
import(graphite)
import(graph)
importClassesFrom(Biobase,ExpressionSet)
importFrom(RBGL,connectedComp)
importFrom(RBGL,floyd.warshall.all.pairs.sp)
importFrom(RBGL,johnson.all.pairs.sp)
importFrom(Rcpp,sourceCpp)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(corpcor,cov.shrink)
importFrom(gRbase,getCliques)
importFrom(gRbase,is.DAG)
importFrom(graphics,abline)
importFrom(graphics,legend)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(parallel,clusterExport)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,parSapply)
importFrom(parallel,stopCluster)
importFrom(stats,cor)
importFrom(stats,cov)
importFrom(stats,density)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,pf)
importFrom(stats,phyper)
importFrom(stats,pnorm)
importFrom(stats,qchisq)
importFrom(stats,qnorm)
importFrom(stats,rbinom)
importFrom(stats,rnorm)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(utils,head)
importMethodsFrom(Biobase,exprs)
importMethodsFrom(Biobase,fData)
importMethodsFrom(Biobase,pData)

importFrom(grDevices, colorRampPalette)
importFrom(graphics, arrows, layout, lines, plot.new,
           plot.window, polygon, strheight, strwidth,
           symbols, title)
importFrom(utils, combn, tail)

useDynLib(ToPASeq)
