useDynLib("crlmm", .registration=TRUE)

 ## this is temporary

 ## exportPattern("^[^\\.]")

 ## 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)

 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
            copyNumber, initializeBigMatrix, initializeBigVector)

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

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

 
 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)

 exportClasses(CNSetLM, ffdf, list)

 exportMethods(open, "[", show, lM, lines, nu, phi, corr, sigma2, tau2)

 exportMethods(CA, CB, totalCopyNumber)

 export(crlmm, 

        crlmmCopynumber, 
        crlmmIllumina, 

        crlmmIllumina2,

        ellipseCenters,

        genotype, 
        readIdatFiles, 

        readIdatFiles2,

        snprma,
        snprma2,

        crlmm2,

        genotype2, genotypeLD,

        batch,

        crlmmCopynumber2, crlmmCopynumberLD)

 export(constructIlluminaCNSet)

 export(linesCNSetLM)

 export(computeCN, fit.lm1, fit.lm2, fit.lm3, fit.lm4, construct,

        dqrlsWrapper, nuphiAllele)

 export(computeCopynumber, ACN)