useDynLib("oligo")

#Generated by codetoolsBioC version 0.0.11
#Timestamp: Thu Mar  4 09:10:56 2010

#Imports: affxparser, affyio, Biobase, DBI, graphics, grDevices,
#         methods, oligoClasses, preprocessCore, splines, stats, utils

importClassesFrom(Biobase, ExpressionSet)

importClassesFrom(methods, array, matrix)

importClassesFrom(oligoClasses, AffySNPPDInfo, DBPDInfo,
                  ExonFeatureSet, ExpressionFeatureSet,
                  ExpressionPDInfo, FeatureSet, GeneFeatureSet,
                  SnpCnvFeatureSet, SnpFeatureSet, TilingFeatureSet,
                  TilingPDInfo)

importMethodsFrom(Biobase, annotation, "annotation<-", channelNames,
                  combine, experimentData, exprs, featureData,
                  "featureData<-", featureNames, "featureNames<-",
                  "notes<-", pData, phenoData, "phenoData<-", preproc,
                  "preproc<-", protocolData, rowMedians, sampleNames,
                  "sampleNames<-", varMetadata)

importMethodsFrom(DBI, dbGetQuery, dbListTables)

importMethodsFrom(oligoClasses, allele, bothStrands, calls, db,
                  genomeBuild, geometry, getA, getM, kind,
                  manufacturer)

importFrom(affxparser, createCel, readCelHeader, readCelIntensities,
           updateCel)

importFrom(affyio, read.celfile.header)

importFrom(Biobase, assayDataElement, assayDataElementReplace,
           assayDataNew)

importFrom(graphics, boxplot, hist, image, lines, matplot, par, plot)

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)

importFrom(preprocessCore, normalize.quantiles,
           normalize.quantiles.determine.target,
           normalize.quantiles.use.target, rma.background.correct)

importFrom(splines, ns)

importFrom(stats, coef, cov, density, dnorm, fitted, kmeans, lm,
           lowess, mad, median, pchisq, quantile, residuals)

importFrom(utils, packageDescription, read.delim, read.table,
           setTxtProgressBar, txtProgressBar, write.table)


## EXPORTS

exportMethods(boxplot, bg, "bg<-", bgSequence, db, exprs, getContainer,
              getPlatformDesign, getX, getY, hist, image, ## initialize,
              MAplot, mm, "mm<-", mmindex, mmSequence, pm, "pm<-", pmChr,
              pmAllele, pmindex, pmFragmentLength, pmOffset, pmPosition,
              pmSequence, pmStrand, probeNames, rma)

export(basecontent, cleanPlatformName, read.celfiles, read.xysfiles,
       sequenceDesignMatrix, list.xysfiles, readSummaries,
       getCrlmmSummaries, getNgsColorsInfo, read.xysfiles2,
       read.celfiles2, basicRMA, darkColors, seqColors,
       getAffinitySplineCoefficients, getBaseProfile)

## Exported functions for CRLMM
export(crlmm, snprma, justSNPRMA, justCRLMM, getPD)
 
## Testing
exportMethods(backgroundCorrect, normalize, summarize, normalizeToTarget)
export(plotM)

## exportMethods(intensity, probesetNames)
