useDynLib("crlmm", .registration=TRUE)

 ##---------------------------------------------------------------------------

 ## Biobase

 ##---------------------------------------------------------------------------

 importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, SnpSet,
 		  NChannelSet, MIAME, Versioned, VersionedBiobase,
 		  Versions)

 importMethodsFrom(Biobase, annotation, "annotation<-",
                   annotatedDataFrameFrom, assayData, "assayData<-",
                   combine, dims, experimentData, "experimentData<-",

                   fData, featureData, "featureData<-", featureNames,

                   fvarMetadata, fvarLabels, pData, "pData<-", phenoData,

                   "phenoData<-", protocolData, "protocolData<-",

                   pubMedIds, rowMedians, sampleNames, snpCall,
                   snpCallProbability,
 		  "snpCall<-", "snpCallProbability<-", storageMode,

                   "storageMode<-", updateObject, varLabels)

 importFrom(Biobase, assayDataElement, assayDataElementNames,

            assayDataElementReplace, assayDataNew, classVersion,
            validMsg)

 ##---------------------------------------------------------------------------

 ## oligoClasses

 ##---------------------------------------------------------------------------

 importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)

 importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,

 		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,

 		  chromosome, position, A, B,

 		  "A<-", "B<-", open, close, flags,

 		  openff, closeff,

 		  batchStatistics, "batchStatistics<-", updateObject,

 		  order, checkOrder)

 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,

            copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)

 importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,

            polygon, rect, segments, text, points, boxplot, lines)

 importFrom(lattice, xyplot, simpleKey, panel.grid, panel.xyplot, lrect, ltext,
 	   lpoints, panel.number, lpolygon)

 
 importFrom(grDevices, grey)

 importFrom(affyio, read.celfile.header, read.celfile)

 importFrom(preprocessCore, normalize.quantiles.use.target, normalize.quantiles)
 importFrom(utils, data, packageDescription, setTxtProgressBar, txtProgressBar)
 importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd, update)

 importFrom(genefilter, rowSds)

 importFrom(mvtnorm, dmvnorm)

 importFrom(ellipse, ellipse)

 importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)

 importClassesFrom(oligoClasses, ff_matrix, ffdf)

 ##exportMethods(lines)

 exportMethods(CA, CB)
 export(crlmm,
        crlmmIllumina,
        crlmmIlluminaV2,
        genotype,

        readIDAT,

        readIdatFiles,

        readGenCallOutput,

        snprma,
        snprma2,

        crlmm2,

        genotype2, genotypeLD,

        genotype.Illumina,

        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)

 export(genotypes, totalCopynumber, rawCopynumber, xyplot)

 exportMethods(A, B, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads,

 	      xyplot, calculateRBaf)

 export(ABpanel, constructInf, preprocessInf, genotypeInf)

 exportClasses(PredictionRegion)