NAMESPACE
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 useDynLib("crlmm", .registration=TRUE)
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 ## this is temporary
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 ## exportPattern("^[^\\.]")
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 ##---------------------------------------------------------------------------
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 ## Biobase
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 ##---------------------------------------------------------------------------
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 importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, SnpSet,
 		  NChannelSet, MIAME, Versioned, VersionedBiobase,
 		  Versions)
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 importMethodsFrom(Biobase, annotation, "annotation<-",
                   annotatedDataFrameFrom, assayData, "assayData<-",
                   combine, dims, experimentData, "experimentData<-",
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                   fData, featureData, "featureData<-", featureNames,
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                   fvarMetadata, fvarLabels, pData, "pData<-", phenoData,
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                   "phenoData<-", protocolData, "protocolData<-",
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                   pubMedIds, rowMedians, sampleNames, snpCall,
                   snpCallProbability,
 		  "snpCall<-", "snpCallProbability<-", storageMode,
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                   "storageMode<-", updateObject, varLabels)
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 importFrom(Biobase, assayDataElement, assayDataElementNames,
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            assayDataElementReplace, assayDataNew, classVersion,
            validMsg)
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 ##---------------------------------------------------------------------------
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 ## oligoClasses
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 ##---------------------------------------------------------------------------
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 importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)
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 importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
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 		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,
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 		  chromosome, position, A, B,
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 		  "A<-", "B<-", open, close, flags,
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 		  batchStatistics, "batchStatistics<-", updateObject)
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 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
            copyNumber, initializeBigMatrix, initializeBigVector)
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 importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
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            polygon, rect, segments, text, points, boxplot, lines)
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 importFrom(grDevices, grey)
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 importFrom(affyio, read.celfile.header, read.celfile)
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 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)
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 importFrom(genefilter, rowSds)
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 importFrom(mvtnorm, dmvnorm)
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 importFrom(ellipse, ellipse)
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 importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
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 ## It is important not to import these classes from oligoClasses
 ## Doing so causes the following errors:
 ## N.AA(container)[index, ] <- someMatrix
 ##Error in function (classes, fdef, mtable)  :
 ##  unable to find an inherited method for function "medianA.AA<-", for signature "CNSet", "ff_matrix"
 ##importClassesFrom(oligoClasses, ffdf, ff_matrix)
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 importClassesFrom(oligoClasses, ff_matrix)
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 ## Important to export these classes
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 ##exportClasses(ff_or_matrix, ff_matrix, ffdf)
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 ##exportClasses(ff_or_matrix)
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 exportMethods(lines)
 exportMethods(CA, CB)
 export(crlmm,
        crlmmIllumina,
        crlmmIlluminaV2,
        genotype,
        readIdatFiles,
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        snprma,
        snprma2,
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        crlmm2,
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        genotype2, genotypeLD,
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
 export(constructIlluminaCNSet)
 export(totalCopynumber)
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
 
 
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 ##export(summarizeNps, genotypeSummary, fit.lm2)