export(

SPIA, DEGraph, clipper, PRS, PWEA, TAPPA, TopologyGSA, CePa,
res, topo.sig, degtable,
AdjacencyMatrix2Pathway,
graphNEL2Pathway,
estimateCF,
reduceGraph,
convertIdentifiersByVector,
KEGG2Pathway,
makeDefaultEdgeData,
prepareTIF, collectWeightsPRS, collectWeightsSPIA,
preparePathways,

AdjacencyMatrix2pathway,
graphNEL2pathway,
KEGG2pathway,
parseKEGG, SPIA4analysis, SPIA2graph
)

useDynLib(ToPASeq)



exportMethods(intersection, join, union, subGraph, clearNode, removeEdge, removeNode, addEdge, addNode, changeDirection, changeInteraction,"nodes<-")

exportMethods(degree, numNoEdges, mostEdges, acc, connComp, edges, isAdjacent, isDirected, isConnected, edgemode, numEdges, numNodes, edgeNames)
exportMethods(convertIdentifiers)


S3method(print, topResult)
S3method(topo.sig, topResult)
S3method(degtable, topResult)
S3method(res, topResult)
S3method(summary, topResult)
S3method(plot,topResult)

import(graphite, gRbase, graph, locfit, methods, Rgraphviz)
importFrom(DESeq2, DESeqDataSetFromMatrix, DESeq, results, estimateSizeFactors, estimateDispersions, nbinomWaldTest, rlogTransformation, varianceStabilizingTransformation)
importFrom(SummarizedExperiment, assay, colData, "colData<-")
importFrom(KEGGgraph, parseKGML, KEGGpathway2Graph, getPathwayInfo, getTitle)
importFrom(AnnotationDbi,select, columns)

importFrom(R.utils, reassignInPackage)
importFrom(edgeR,DGEList, calcNormFactors)

importFrom(parallel, detectCores, makeCluster, clusterExport, parSapply, stopCluster)
importClassesFrom(Biobase, ExpressionSet)
importMethodsFrom(Biobase, exprs, pData)

importFrom(DESeq, newCountDataSet, estimateSizeFactors, estimateDispersions)
importFrom(fields, image.plot)
importFrom(TeachingDemos, shadowtext)
importFrom(limma,  lmFit, makeContrasts, contrasts.fit, eBayes, decideTests, topTable, voom) 
importMethodsFrom(graph, edgeData, edgeDataDefaults)

import(doParallel)

importFrom(qpgraph,qpIPF)
importFrom(RBGL,johnson.all.pairs.sp)
importFrom(clipper, easyClip, pathQ, cliqueMeanTest, cliqueVarianceTest)
