NAMESPACE

import(limma)
import(DNAcopy)
import(preprocessCore)
import(marray)
import(sva)
import(IlluminaHumanMethylation450kmanifest)
import(minfi)
import(ChAMPdata)
import(Illumina450ProbeVariants.db)
import(wateRmelon)
import(plyr)
import(GenomicRanges)
import(isva)
import(qvalue)
import(bumphunter)
import(doParallel)
import(quadprog)
import(shiny)
import(shinythemes)
import(plotly)
import(RColorBrewer)
import(DMRcate)
import(dendextend)
import(sva)
import(IlluminaHumanMethylationEPICmanifest)
import(FEM)
import(impute)
import(goseq)
import(combinat)
import(illuminaio)
import(IlluminaHumanMethylationEPICanno.ilm10b2.hg19)
import(rmarkdown)
import(missMethyl)
import(Hmisc)
import(globaltest)
import(kpmt,"kpmt")
import(ggplot2)

importFrom("utils", "read.csv")
importFrom(RPMM, blc)

importFrom("grDevices", "dev.off", "jpeg", "pdf", "rainbow")
importFrom("graphics", "axis", "legend", "mtext", "par", "plot",
            "segments", "title")
importFrom("stats", "C", "cor", "density", "dist", "dnorm", "hclust",
            "kruskal.test", "lm", "model.matrix", "na.omit", "p.adjust",
            "pbeta", "pnorm", "pt", "qbeta", "qnorm", "qqline",
            "qqnorm", "qqplot", "quantile", "rbeta", "rgamma",
                                                          "rmultinom", "sd", "var")
importFrom("utils", "capture.output", "data", "head", "read.delim",
            "read.table", "write.table")

importFrom("grDevices", "colorRampPalette")
importFrom("stats", "aggregate", "as.dendrogram", "as.formula","bartlett.test",
           "cmdscale", "fisher.test", "fitted","loess", "order.dendrogram", "t.test")

export(
	champ.process, 
    champ.load,
    champ.import,
    champ.filter,
	champ.impute, 
    champ.QC,
    champ.norm,
    champ.SVD,
    champ.runCombat,
	champ.DMP, 
	champ.DMR, 
	champ.Block, 
	champ.GSEA, 
    champ.ebGSEA,
	champ.EpiMod,
    champ.CNA,
    champ.refbase,
    DMP.GUI,
    DMR.GUI,
    QC.GUI,
    CpG.GUI,
    Block.GUI
	)