useDynLib(R3CPET,.registration=TRUE)
## Exports ###

exportMethods(loadPETs, pet, tfbs, loadTFBS, loadPPI, ppi,
              "pet<-", "tfbs<-", "ppi<-",createIndexes, 
              PrepareData, CreateCenteredBED,buildNetworks,
              networks, sizes, TF, InferNetworks,clusterInteractions,
              getClusters, getRegionsIncluster, getRegionsInNetwork,
              topEdges, topNodes, wordsPerTopic,docPerTopic, betas,
              updateResults, outputGenesPerClusterToDir, outputGenesPerNetworkToDir,
              GOEnrich.folder, GOEnrich.networks, GenerateNetworks,
              annotateExpression, plot3CPETRes, visualizeCircos,
              visualizeInteractions, plotTrack, createServer)

exportClasses(cluesOrSota, ChiapetExperimentData,
			  NetworkCollection, HLDAResult, ChromMaintainers)

export(ChiapetExperimentData, NetworkCollection, 
		HLDAResult, ChromMaintainers)
#exportPattern("^[[:alpha:]]+")

### imports ####
import(methods)
#import(biovizBase)
#import(ChIPpeakAnno)

importFrom(clues, clues)
importFrom(clues, plotCurves) 
importFrom(clues, plotClusters) 
importFrom(clues, plotAvgCurves) 

importFrom(clValid, sota)

importFrom(data.table, SJ)
importFrom(data.table, setkey)
importFrom(data.table, data.table)

importFrom(parallel, mclapply)
importFrom(parallel, parLapply)
importFrom(parallel, makeCluster)
importFrom(parallel, detectCores)
importFrom(parallel, stopCluster)

importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(GenomicRanges,GRangesList)
importClassesFrom(GenomicRanges,GenomicRanges)
importClassesFrom(GenomicRanges,GenomicRangesList)
importFrom(GenomicRanges, GRanges)
importMethodsFrom(GenomicRanges, end)
importMethodsFrom(GenomicRanges, start)
importMethodsFrom(GenomicRanges, mcols)
importMethodsFrom(GenomicRanges, values)
importMethodsFrom(GenomicRanges, setdiff)
importMethodsFrom(GenomicRanges, seqinfo)
importMethodsFrom(GenomicRanges, seqnames)
importMethodsFrom(GenomicRanges, promoters)
importMethodsFrom(GenomicRanges, intersect)
importMethodsFrom(GenomicRanges, seqlengths)
importMethodsFrom(GenomicRanges, findOverlaps)
importMethodsFrom(GenomicRanges, keepSeqlevels)
importMethodsFrom(GenomicRanges, seqlevels)
importMethodsFrom(GenomicRanges, "seqlengths<-")
importMethodsFrom(GenomicRanges, elementMetadata)
importMethodsFrom(GenomicRanges, subsetByOverlaps)


importFrom(S4Vectors, Rle)
importFrom(S4Vectors,DataFrame)
importClassesFrom(IRanges, Views)
importClassesFrom(IRanges, IRanges)
importClassesFrom(IRanges, RleList)
importClassesFrom(IRanges,RangesList)
importClassesFrom(IRanges,RangedData)
importClassesFrom(IRanges,IntegerList)
importClassesFrom(IRanges,CharacterList)
importClassesFrom(IRanges, IRangesList)

importFrom(IRanges, Views)
importFrom(IRanges, RleList)
importFrom(IRanges, IRanges)
importFrom(IRanges,RangesList)
importFrom(IRanges,RangedData)
importFrom(IRanges,IntegerList)
importFrom(IRanges,CharacterList)
importFrom(IRanges, IRangesList)

importMethodsFrom(IRanges, width)
importMethodsFrom(IRanges,queryHits)
importMethodsFrom(IRanges,"values<-")
importMethodsFrom(IRanges,subjectHits)
importMethodsFrom(IRanges,elementLengths)

importFrom(igraph, V)
importFrom(igraph, E)
importFrom(igraph, 'V<-')
importFrom(igraph, degree)
importFrom(igraph, vcount)
importFrom(igraph, ecount)
importFrom(igraph, vertex)
importFrom(igraph, simplify)
importFrom(igraph, is.igraph)
importFrom(igraph, get.edges)
importFrom(igraph, read.graph)
importFrom(igraph, write.graph)
importFrom(igraph, graph.empty)
importFrom(igraph, get.edgelist)
importFrom(igraph, get.adjacency)
importFrom(igraph, as.undirected)
importFrom(igraph, delete.vertices)
importFrom(igraph, induced.subgraph)
importFrom(igraph, layout.kamada.kawai)
importFrom(igraph, get.all.shortest.paths)

importFrom(ggbio, xlim)
importFrom(ggbio, tracks)
importFrom(ggbio, plotIdeogram)
importFrom(ggbio, layout_circle)

importFrom(ggplot2, aes)
importFrom(ggplot2, theme)
importFrom(ggplot2, ggsave)
importFrom(ggplot2, ggplot)
importFrom(ggplot2, ggtitle)
importFrom(ggplot2, autoplot)
importFrom(ggplot2, geom_bar)
importFrom(ggplot2, theme_bw)
importFrom(ggplot2, geom_text)
importFrom(ggplot2, geom_path)
importFrom(ggplot2, scale_size)
importFrom(ggplot2, geom_point)
importFrom(ggplot2, coord_flip)
importFrom(ggplot2, aes_string)
importFrom(ggplot2, element_rect)
importFrom(ggplot2, element_text)
importFrom(ggplot2, element_blank)
importFrom(ggplot2, scale_y_continuous)
importFrom(ggplot2, scale_colour_gradient)

#importFrom(biomaRt, getBM)
#importFrom(biomaRt, useMart)
#importFrom(biomaRt, useDataset)


#importFrom(org.Hs.eg.db, org.Hs.egUCSCKG)
#importFrom(org.Hs.eg.db, org.Hs.eg.db)

#importFrom(AnnotationDbi, select)
#importFrom(AnnotationDbi, toTable)


#importFrom(TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene)
importFrom(Hmisc, bezier)
importFrom(DAVIDQuery, DAVIDQuery)
importFrom(pheatmap, pheatmap)
importFrom(reshape2, melt)
#importFrom(shiny, runApp)
importFrom(Rcpp, evalCpp)
