useDynLib("crlmm", .registration=TRUE)

 
 ##importClassesFrom(methods, ANY, character, data.frame, "function", integer, matrix, numeric)
 
 importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet,

 		  SnpSet, NChannelSet, MIAME, Versioned, VersionedBiobase, Versions)

 
 importClassesFrom(oligoClasses, SnpLevelSet)
 
 importMethodsFrom(Biobase, annotation, "annotation<-", annotatedDataFrameFrom,
 		  assayData, "assayData<-", combine,
 		  experimentData, "experimentData<-",
                   fData, featureData, "featureData<-", featureNames,
 		  fvarMetadata, fvarLabels,
                   pData, phenoData, "phenoData<-", pubMedIds, rowMedians, sampleNames, scanDates,

                   "scanDates<-", storageMode, "storageMode<-", updateObject)

 
 
 ##importMethodsFrom(oligoClasses, chromosome, copyNumber, position)
 importFrom(oligoClasses, chromosome, copyNumber, position, calls)
 
 ##importMethodsFrom(methods, initialize, show)
 
 ##importFrom(methods, "@<-", callNextMethod, new, validObject)
 
 importFrom(Biobase, assayDataElement, assayDataElementNames,
            assayDataElementReplace, assayDataNew, classVersion)
 
 importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
            polygon, rect, segments, text, points)
 
 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)

 importFrom(genefilter, rowSds)

 importFrom(mvtnorm, dmvnorm)

 
 importFrom(ellipse, ellipse)
 

 S3method(ellipse,CopyNumberSet)
 

 exportClasses(ABset, CopyNumberSet, CrlmmSetList)
 ##S3method(ellipse, CopyNumberSet)

 exportMethods(A, B,
 	      calls,

 	      CA,
 	      "CA<-",
 	      CB,
 	      "CB<-",
 	      cnIndex,
 	      confs,
 	      plot,
 	      points,
 	      show,
 	      snpIndex)
 
 export(celDates,
        calls,
        chromosome,
        cnrma,
        combine,
        computeCopynumber,
        copyNumber,
        crlmm,
        crlmmIllumina,
        crlmmWrapper,
        ellipse,
        computeEmission,
        list.celfiles,
        position,
        readIdatFiles,
        sampleNames,
        scanDates,
        "scanDates<-",
        snprma)