useDynLib("crlmm", .registration=TRUE)

 importClassesFrom(Biobase, AssayData, eSet)
 
 importClassesFrom(methods, ANY, character, formula, integer, list,
                   matrix, oldClass)
 importFrom(methods, setOldClass)
 
 ## importClassesFrom(oligoClasses, CNSet, CNSetLM, ff_matrix,
 ##                   ff_or_matrix, oligoSnpSet)
 importClassesFrom(oligoClasses, CNSet, oligoSnpSet, ff_or_matrix)
 ##setOldClass(ff_or_matrix)
 
 importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation,
                   assayData, experimentData, featureData,
                   "featureData<-", featureNames, "featureNames<-",
                   pData, "pData<-", phenoData, "phenoData<-",
                   protocolData, "protocolData<-", rowMedians,
                   sampleNames, snpCall, "snpCall<-",
                   snpCallProbability, "snpCallProbability<-",
                   storageMode, "storageMode<-", varLabels)
 
 importMethodsFrom(BiocGenerics, cbind, colnames, Filter, get,
                   intersect, lapply, ncol, NCOL, nrow, NROW, order,
                   paste, pmax, pmin, rbind, rownames, sapply, setdiff,
                   table, union, unique)
 
 importMethodsFrom(genefilter, show)
 
 importMethodsFrom(oligoClasses, A, "A<-", B, batch, batchNames,
                   batchStatistics, "batchStatistics<-", calls,
                   chromosome, close, confs, flags, isSnp, mean, nu,
                   open, phi, "sampleNames<-")
 
 importFrom(affyio, read.celfile, read.celfile.header)
 
 importFrom(Biobase, assayDataElement, assayDataElementReplace,
            assayDataNew, copyEnv)
 

 importFrom(ellipse, ellipse)

 
 importFrom(genefilter, rowSds)
 
 importFrom(lattice, lpolygon, panel.grid, panel.number, panel.xyplot,
            xyplot)
 
 importFrom(methods, "@<-", as, callNextMethod, is, new, validObject)
 
 importFrom(mvtnorm, rmvnorm)
 
 importFrom(oligoClasses, celfileDate, chromosome2integer, i2p,
            initializeBigMatrix, initializeBigVector, integerMatrix,
 	   isPackageLoaded,
            ldPath, ocLapply, ocProbesets, ocSamples,
 	   parStatus,

            splitIndicesByLength, splitIndicesByNode, AssayDataList)

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

 ## foreach
 import(foreach)
 

 ##----------------------------------------------------------------------------
 ## export
 ##----------------------------------------------------------------------------
 exportClasses(PredictionRegion)

 exportMethods(CA, CB,

 	      A, B, corr, nuA, nuB, phiA, phiB,
 	      predictionRegion, posteriorProbability,
 	      tau2, Ns, medians, mads,
 	      xyplot, calculateRBaf)

 export(crlmm,
        crlmmIllumina,
        crlmmIlluminaV2,

        constructAffyCNSet,

        genotype,

        genotypeAffy,

        readIDAT,

        readIdatFiles,

        readGenCallOutput,

        snprma,
        snprma2,

        cnrmaAffy,
        snprmaAffy,

        crlmm2,

        genotype2, genotypeLD,

        genotypeAffy,

        genotype.Illumina,

        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)

 export(genotypes, totalCopynumber, rawCopynumber, xyplot)

 export(ABpanel, validCEL, celDates, validCdfNames)