## crlmm NAMESPACE
useDynLib("crlmm", .registration=TRUE)

## Biobase
importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, SnpSet,
		  NChannelSet, MIAME, Versioned, VersionedBiobase,
		  Versions)

importMethodsFrom(Biobase, annotation, "annotation<-",
                  annotatedDataFrameFrom, assayData, "assayData<-",
		  snpCallProbability,
                  combine, dims, experimentData, "experimentData<-",
                  fData, featureData, "featureData<-", featureNames,
                  fvarMetadata, fvarLabels, pData, phenoData,
                  "phenoData<-", protocolData, "protocolData<-",
                  pubMedIds, rowMedians, sampleNames, snpCall, storageMode,
                  "storageMode<-", updateObject, varLabels)

importFrom(Biobase, assayDataElement, assayDataElementNames,
           assayDataElementReplace, assayDataNew, classVersion,
           validMsg)

## oligoClasses
##importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)

##S3 method ffdf and class ffdf
importFrom(ff, ffdf, ff, as.ff, as.ffdf)



##importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
##		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,
##		  chromosome, position, CA, "CA<-", CB, "CB<-", A, B)

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

## graphics
importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
           polygon, rect, segments, text, points, boxplot)

## grDevices
importFrom(grDevices, grey)

## affyio
importFrom(affyio, read.celfile.header, read.celfile)

## preprocessCore
importFrom(preprocessCore, normalize.quantiles.use.target,
           normalize.quantiles)

## utils
importFrom(utils, data, packageDescription, setTxtProgressBar,
           txtProgressBar)

## stats
importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile,
           sd, update)

## genefilter
importFrom(genefilter, rowSds)

## mvtnorm
importFrom(mvtnorm, dmvnorm)

## ellipse
importFrom(ellipse, ellipse)


##exportClasses(FFSet)
exportMethods(annotatedDataFrameFrom,
	copyNumber, initialize, 
              ##show, "$", "[[", "[", 
	      genomeAnnotation,
	      lM,
	      CA,
	      CB,
	      A,
	      B,
	      snpCall,
	      confs,
	      chromosome,
	      position,
	      isSnp)
export(crlmmOptions, crlmm, crlmmCopynumber, ellipse, readIdatFiles, snprma, getParam, validCdfNames)



#############
## TO REMOVE
#############

##export everything that does not start with a .
exportPattern("^[^\\.]")