NAMESPACE
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 useDynLib("crlmm", .registration=TRUE)
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 importClassesFrom(Biobase, AssayData, eSet)
 
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 ##importClassesFrom(methods, ANY, character, formula, integer, list,
 ##                  matrix, oldClass)
 ##importMethodsFrom(methods, initialize, show)
 import(methods)
 ##importFrom(methods, setOldClass)
 ##importFrom(methods, as, callNextMethod, is, new, validObject)
 ##importFrom(methods, callNextMethod, new, validObject, coerce)
 
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 importFrom(RcppEigen, fastLmPure)
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 ## importClassesFrom(oligoClasses, CNSet, CNSetLM, ff_matrix,
 ##                   ff_or_matrix, oligoSnpSet)
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 importClassesFrom(oligoClasses, CNSet, oligoSnpSet, ff_or_matrix, GenomeAnnotatedDataFrame)
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 ##setOldClass(ff_or_matrix)
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 import(matrixStats)
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 importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation,
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                   AnnotatedDataFrame, assayData, experimentData, featureData,
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                   "featureData<-", featureNames, "featureNames<-",
                   pData, "pData<-", phenoData, "phenoData<-",
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                   protocolData, "protocolData<-",
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                   sampleNames, snpCall, "snpCall<-",
                   snpCallProbability, "snpCallProbability<-",
                   storageMode, "storageMode<-", varLabels)
 
 importMethodsFrom(BiocGenerics, cbind, colnames, Filter, get,
                   intersect, lapply, ncol, NCOL, nrow, NROW, order,
                   paste, pmax, pmin, rbind, rownames, sapply, setdiff,
                   table, union, unique)
 
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 ##importMethodsFrom(genefilter, show)
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 importMethodsFrom(oligoClasses, A, "A<-", B, batch, batchNames,
                   batchStatistics, "batchStatistics<-", calls,
                   chromosome, close, confs, flags, isSnp, mean, nu,
                   open, phi, "sampleNames<-")
 
 importFrom(affyio, read.celfile, read.celfile.header)
 
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 importFrom(illuminaio, readIDAT)
 
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 importFrom(Biobase, assayDataElement, assayDataElementReplace,
            assayDataNew, copyEnv)
 
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 importFrom(ellipse, ellipse)
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 ##importFrom(genefilter, rowSds)
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 importFrom(lattice, lpolygon, panel.grid, panel.number, panel.xyplot,
            xyplot)
 
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 ##importFrom(methods, as, callNextMethod, is, new, validObject)
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 importFrom(mvtnorm, rmvnorm)
 
 importFrom(oligoClasses, celfileDate, chromosome2integer, i2p,
            initializeBigMatrix, initializeBigVector, integerMatrix,
 	   isPackageLoaded,
            ldPath, ocLapply, ocProbesets, ocSamples,
 	   parStatus,
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            splitIndicesByLength, splitIndicesByNode, AssayDataList)
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 importFrom(preprocessCore, normalize.quantiles, normalize.quantiles.determine.target,
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            normalize.quantiles.use.target, subColSummarizeMedian)
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 importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile,
            sd)
 
 importFrom(utils, packageDescription, setTxtProgressBar,
            txtProgressBar)
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 importFrom(graphics, plot, smoothScatter, abline)
 
 importFrom(beanplot, beanplot)
 
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 ## foreach
 import(foreach)
 
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 importFrom(VGAM, vglm, multinomial, coefficients)
 
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 importFrom(parallel, makeCluster, detectCores, parRapply, stopCluster, clusterEvalQ, parCapply)
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 importFrom(limma, loessFit)
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 ##----------------------------------------------------------------------------
 ## export
 ##----------------------------------------------------------------------------
 exportClasses(PredictionRegion)
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 exportMethods(CA, CB,
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 	      A, B, corr, nuA, nuB, phiA, phiB,
 	      predictionRegion, posteriorProbability,
 	      tau2, Ns, medians, mads,
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 	      xyplot, calculateRBaf, OligoSetList,
 	      BafLrrSetList)
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 export(crlmm,
        crlmmIllumina,
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        constructAffyCNSet,
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        genotype,
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        genotypeAffy,
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        readIdatFiles,
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        readGenCallOutput,
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        snprma,
        snprma2,
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        cnrmaAffy,
        snprmaAffy,
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        crlmm2,
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        genotype2, genotypeLD,
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        genotypeAffy,
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        genotype.Illumina,
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        plotSamples, plotSNPs,
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        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
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 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
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 export(ABpanel, validCEL, celDates, validCdfNames)
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 ##export(constructOligoSetListFrom, constructBafLrrSetListFrom)