useDynLib("oligo") ###################################### ## Importing: Classes ###################################### importClassesFrom(Biobase, ExpressionSet) importClassesFrom(methods, array, matrix, ANY, character, integer, missing, numeric) importClassesFrom(oligoClasses, AffySNPPDInfo, DBPDInfo, ExonFeatureSet, ExpressionFeatureSet, ExpressionPDInfo, FeatureSet, GeneFeatureSet, SnpCnvFeatureSet, SnpFeatureSet, TilingFeatureSet, TilingPDInfo) ###################################### ## Importing: Methods ###################################### importMethodsFrom(Biobase, channel, channelNames, combine, description, experimentData, "experimentData<-", exprs, "exprs<-", featureData, "featureData<-", featureNames, "featureNames<-", "notes<-", pData, "pData<-", phenoData, "phenoData<-", preproc, "preproc<-", protocolData, "protocolData<-", rowMedians, sampleNames, "sampleNames<-", varMetadata, "varMetadata<-", varLabels) importMethodsFrom(DBI, dbGetQuery, dbListFields, dbListTables) importMethodsFrom(oligoClasses, allele, bothStrands, calls, db, genomeBuild, geometry, getA, getM, kind, manufacturer) importMethodsFrom(BiocGenerics, ncol, boxplot, residuals, image, weights, 'annotation<-', annotation, normalize) importMethodsFrom(stats4, coef, plot) importMethodsFrom(RSQLite, dbDisconnect) importFrom(graphics, abline, frame, mtext, smoothScatter, text) importFrom(stats, IQR, aggregate, approx, complete.cases, loess, predict, rnorm, smooth.spline, splinefun) importFrom(utils, data) ###################################### ## Importing: Functions ###################################### importFrom(affxparser, createCel, readCelHeader, readCelIntensities, updateCel) importFrom(affyio, read.celfile.header, read.celfile) importFrom(Biobase, assayData, assayDataElement, assayDataElementReplace, assayDataNew, assayDataElementNames) importFrom(BiocGenerics, boxplot, image, ncol, residuals, annotation, "annotation<-") importFrom(graphics, hist, lines, matplot, par) importFrom(grDevices, colorRampPalette, gray) importFrom(methods, callNextMethod, is, new, slot, "slot<-", validObject) importFrom(oligoClasses, list.celfiles, requireAnnotation, isPackageLoaded, setCluster, delCluster, getCluster, ocProbesets, ocSamples, ocLapply, splitIndicesByLength, splitIndicesByNode, getBar, createFF, ldPath, ldStatus) importFrom(preprocessCore, normalize.quantiles, normalize.quantiles.determine.target, normalize.quantiles.use.target, normalize.quantiles.in.blocks, normalize.quantiles.robust, rma.background.correct, rcModelPLM, rcModelPLMr, rcModelPLMrr, rcModelPLMrc, rcModelWPLM, rcModelWPLMr, rcModelWPLMrr, rcModelWPLMrc, rcModelMedianPolish, subrcModelPLM, subrcModelMedianPolish) importFrom(splines, ns) importFrom(stats, cov, density, dnorm, fitted, kmeans, lm, lowess, mad, median, pchisq, quantile) importFrom(utils, packageDescription, read.delim, read.table, setTxtProgressBar, txtProgressBar, write.table) importFrom(Biostrings, letterFrequency) importFrom(ff, ff, ffvecapply, clone.ff, clone.ffdf, filename, is.ff, 'finalizer<-', vmode) ##importFrom(ff, open, finalizer, close, 'finalizer<-', delete) import(zlibbioc) ## EXPORTS exportMethods(boxplot, bg, "bg<-", bgSequence, db, exprs, "exprs<-", getContainer, getPlatformDesign, getX, getY, hist, image, MAplot, mm, "mm<-", mmindex, mmSequence, pm, "pm<-", pmChr, pmAllele, pmindex, pmFragmentLength, pmOffset, pmPosition, pmSequence, pmStrand, probeNames, rma, runDate, getNetAffx) export(basecontent, cleanPlatformName, read.celfiles, read.xysfiles, sequenceDesignMatrix, list.xysfiles, readSummaries, getCrlmmSummaries, getNgsColorsInfo, read.xysfiles2, read.celfiles2, basicRMA, darkColors, seqColors, seqColors2, divColors, getAffinitySplineCoefficients, getBaseProfile, basicPLM, getProbeInfo, availProbeInfo) ## Exported functions for CRLMM export(crlmm, snprma, justSNPRMA, justCRLMM, getPD) ## Testing exportMethods(backgroundCorrect, normalize, summarize, normalizeToTarget) export(plotM, backgroundCorrectionMethods, normalizationMethods) exportMethods(intensity, probesetNames) ## PLM export("NUSE", "RLE") exportMethods("paCalls") exportClasses(oligoPLM) exportMethods(ncol, nprobes, nprobesets, coef, coefs.probe, weights, residuals, se, se.probe, residualSE, geometry, method, manufacturer, annotation, show, boxplot, image, opset2eset) export('fitProbeLevelModel', 'summarizationMethods')