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, 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, CA, "CA<-", CB, "CB<-", A, B, "A<-", "B<-")

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

 importFrom(oligoClasses, copyNumber)

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

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

 
 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)
 

 exportClasses(CNSetLM)
 exportMethods(copyNumber, open, "[", show, lM, "lM<-")
 export(crlmm, 
 	      crlmmCopynumber, 
 	      crlmmIllumina, 
 	      crlmmIlluminaRS, 
 	      ellipse, 
 	      genotype, 
 	      getParam, 
 	      readIdatFiles, 
 	      snprma) 
 
 export(initializeBigMatrix, initializeParamObject)