## 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<-",
                  combine, dims, experimentData, "experimentData<-",
                  fData, featureData, "featureData<-", featureNames,
                  fvarMetadata, fvarLabels, pData, phenoData,
                  "phenoData<-", protocolData, "protocolData<-",
                  pubMedIds, rowMedians, sampleNames, storageMode,
                  "storageMode<-", updateObject, varLabels)

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

## oligoClasses
importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet)

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

exportMethods(copyNumber)
export(cnOptions, crlmm, crlmmIllumina, crlmmCopynumber, ellipse, readIdatFiles, snprma, getParam) 

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

##export(thresholdModelParams, computeCopynumber.CNSet, nuphiAllele, coefs, biasAdjNP, 
##       nonpolymorphic.poe, crlmmWrapper,
##       loadIlluminaCallSet, loadIlluminaRG, loadIlluminaCnrma,
##       cnrma, 
##       crlmmGT, oneBatch)