import(parallel)
import(doParallel)
import(foreach)
import(stats)
import(SummarizedExperiment)
importFrom(IRanges,IRanges,reduce,start,end,width)
importFrom(S4Vectors,metadata,SimpleList)
importFrom(illuminaio,readIDAT)
importFrom(matrixStats, colMedians,colMads)
importFrom(grDevices,dev.off,jpeg,colorRampPalette, pdf)
importFrom("grDevices", "postscript")
importFrom(graphics,abline,axis,boxplot,hist,legend,
    lines,par,plot,polygon,text,points,mtext)
importFrom(methods, as, callNextMethod, is, new)
importFrom(utils, read.table,write.table,head,tail,write.csv)
importFrom(geneplotter,multidensity)
importFrom(impute,impute.knn)
importFrom(RPMM,blc,betaObjf)
importFrom(dynamicTreeCut,printFlush)
importFrom(minfi,getProbeInfo,getManifestInfo,getControlAddress,
    detectionP,preprocessRaw,getAnnotation,featureNames,
    getProbeType)
importFrom(Biobase,featureNames,rowMedians)
importFrom(ExperimentHub,ExperimentHub)
importFrom(AnnotationHub,query)
importFrom(genefilter,rowFtests,rowttests)
importFrom(gplots,heatmap.2)
importFrom(quadprog,solve.QP)
importFrom(gtools,mixedsort)
importFrom(irlba,prcomp_irlba)

exportClasses(rgDataSet,methDataSet)

export(preprocessENmix,
    nmode,norm.quantile,plotCtrl,
    QCinfo,pcrplot,freqpoly,multifreqpoly,
    qcfilter,rcp,oxBS.MLE,ctrlsva,relic,mpreprocess,
    getB,B2M,M2B,rgDataSet,methDataSet,repicc,
    calcdetP,getCGinfo,getmeth,readidat,dupicc,
    readmanifest,estimateCellProp,predSex,methyAge,
    combp,ipdmr,mhtplot,p.qqplot,simubed,methscore,rm.cgsuffix,rcp2)

