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)

### imports ####
import(methods)



importFrom("grDevices", "colorRampPalette", 
            "colors", "dev.off",
            "gray", "pdf", "png")
             
importFrom("graphics", "par", "plot")
importFrom("stats", "quantile")
importFrom("utils", "data", "head", 
            "read.csv", "read.delim",
            "read.table", "tail", "write.table")


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)

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(ggplot2, aes)
importFrom(ggplot2, theme)
importFrom(ggplot2, ggsave)
importFrom(ggplot2, ggplot)
importFrom(ggplot2, ggtitle)
importFrom(ggplot2, autoplot)
importFrom(ggplot2, geom_bar)
importFrom(ggplot2, Position)
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(ggbio, xlim)
importFrom(ggbio, tracks)
importFrom(ggbio, plotIdeogram)
importFrom(ggbio, layout_circle)




importFrom(S4Vectors, Rle)
importFrom(S4Vectors, mcols)
importFrom(S4Vectors, values)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,"values<-")
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,elementNROWS)




importClassesFrom(IRanges, Views)
importClassesFrom(IRanges, IRanges)
importClassesFrom(IRanges, RleList)
importClassesFrom(IRanges,IntegerRangesList)
importClassesFrom(IRanges,IntegerList)
importClassesFrom(IRanges,CharacterList)
importClassesFrom(IRanges, IRangesList)

importFrom(IRanges, Views)
importFrom(IRanges, RleList)
importFrom(IRanges, IRanges)
importFrom(IRanges,IntegerList)
importFrom(IRanges,CharacterList)
importFrom(IRanges, IRangesList)
importFrom(IRanges,subsetByOverlaps)

importMethodsFrom(IRanges, width)


importFrom(GenomeInfoDb,keepSeqlevels)
importFrom(GenomeInfoDb, seqlevels)
importFrom(GenomeInfoDb, seqlengths)
importFrom(GenomeInfoDb,"seqlengths<-")

importClassesFrom(GenomicRanges,GRanges)
importClassesFrom(GenomicRanges,GRangesList)
importClassesFrom(GenomicRanges,GenomicRanges)
importClassesFrom(GenomicRanges,GenomicRangesList)
importFrom(GenomicRanges, GRanges)
importMethodsFrom(GenomicRanges, end)
importMethodsFrom(GenomicRanges, start)
importMethodsFrom(GenomicRanges, setdiff)
importMethodsFrom(GenomicRanges, seqinfo)
importMethodsFrom(GenomicRanges, seqnames)
importMethodsFrom(GenomicRanges, promoters)
importMethodsFrom(GenomicRanges, intersect)
importMethodsFrom(GenomicRanges, findOverlaps)
importMethodsFrom(GenomicRanges, elementMetadata)



#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(pheatmap, pheatmap)
importFrom(reshape2, melt)
#importFrom(shiny, runApp)
importFrom(Rcpp, evalCpp)
importFrom(RCurl, getURL)
importFrom(RCurl, getCurlHandle)
