useDynLib("crlmm", .registration=TRUE)

 importClassesFrom(Biobase, AssayData, eSet)
 

 ##importClassesFrom(methods, ANY, character, formula, integer, list,
 ##                  matrix, oldClass)
 ##importMethodsFrom(methods, initialize, show)
 import(methods)
 ##importFrom(methods, setOldClass)
 ##importFrom(methods, as, callNextMethod, is, new, validObject)
 ##importFrom(methods, callNextMethod, new, validObject, coerce)
 

 importFrom(RcppEigen, fastLmPure)

 ## importClassesFrom(oligoClasses, CNSet, CNSetLM, ff_matrix,
 ##                   ff_or_matrix, oligoSnpSet)

 importClassesFrom(oligoClasses, CNSet, oligoSnpSet, ff_or_matrix, GenomeAnnotatedDataFrame)

 ##setOldClass(ff_or_matrix)

 import(matrixStats)

 
 importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation,

                   AnnotatedDataFrame, assayData, experimentData, featureData,

                   "featureData<-", featureNames, "featureNames<-",
                   pData, "pData<-", phenoData, "phenoData<-",

                   protocolData, "protocolData<-",

                   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(illuminaio, readIDAT)
 

 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, genomeBuild, celfileName)

 importFrom(preprocessCore, normalize.quantiles, normalize.quantiles.determine.target,

            normalize.quantiles.use.target, subColSummarizeMedian)

 
 importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile,
            sd)
 
 importFrom(utils, packageDescription, setTxtProgressBar,
            txtProgressBar)

 importFrom(graphics, plot, smoothScatter, abline)
 
 importFrom(beanplot, beanplot)
 

 ## foreach
 import(foreach)
 

 importFrom(VGAM, vglm, multinomial, coefficients)
 

 importFrom(parallel, makeCluster, detectCores, parRapply, stopCluster, clusterEvalQ, parCapply)

 importFrom(limma, loessFit)

 importFrom(ff, delete)
 

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

 exportMethods(CA, CB,

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

 	      xyplot, calculateRBaf, OligoSetList,
 	      BafLrrSetList)

 export(crlmm,
        crlmmIllumina,

        constructAffyCNSet,

        genotype,

        genotypeAffy,

        readIdatFiles,

        readGenCallOutput,

        snprma,
        snprma2,

        cnrmaAffy,
        snprmaAffy,

        crlmm2,

        genotype2, genotypeLD,

        genotypeAffy,

        genotype.Illumina,

        plotSamples, plotSNPs,

        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)

 export(genotypes, totalCopynumber, rawCopynumber, xyplot)

 export(ABpanel, validCEL, celDates, validCdfNames)

 
 ##export(constructOligoSetListFrom, constructBafLrrSetListFrom)