Package: ACME Exports: do.aGFF.calc, findRegions, read.resultsGFF, findClosestGene, write.sgr, getRefflat ExportMethods: show, print, plot ExportClasses: aGFF, aGFFCalc Package: AffyCompatible ExportMethods: show Package: AffyExpress Exports: AffyInteraction, AffyQA, AffyRegress, Filter, interaction.result2html, make.contrast, make.design, post.interaction, pre.process, regress, result2html, select.sig.gene, import.data Package: AnnBuilder Exports: ABPkgBuilder, athPkgBuilder, chrLocPkgBuilder, cMapPathBuilder, GOPkgBuilder, homoPkgBuilder, KEGGPkgBuilder, SPPkgBuilder, yeastPkgBuilder, writeSourceUrlConfig, readSourceUrlConfig, downloadSourceData, makeSrcInfo, map2LL, getSrcUrl, queryGEO, parseData, loadFromUrl, readData, createEmptyDPkg, parser, EG, GEO, UG, KEGG, GP, IPI, YEAST, GO, PFAM, srcUrl, baseFile, getFileExt, pfamBuilder, resolveMaps, getSrcUrl ExportClasses: EG, GEO, UG, GO, KEGG, GP, IPI, YEAST, PFAM, pubRepo Package: AnnotationDbi Exports: showQCData, debugSQL, GOTerms, dbFileConnect, dbFileDisconnect, mergeToNamespaceAndExport, createAnnObjs.HUMANCHIP_DB, createAnnObjs.MOUSECHIP_DB, createAnnObjs.RATCHIP_DB, createAnnObjs.FLYCHIP_DB, createAnnObjs.YEASTCHIP_DB, createAnnObjs.ARABIDOPSISCHIP_DB, createAnnObjs.HUMAN_DB, createAnnObjs.MALARIA_DB, createAnnObjs.MOUSE_DB, createAnnObjs.RAT_DB, createAnnObjs.FLY_DB, createAnnObjs.YEAST_DB, createAnnObjs.YEASTLEGACY_DB, createAnnObjs.GO_DB, createAnnObjs.KEGG_DB, createAnnObjs.INPARANOIDHOMSA_DB, createAnnObjs.INPARANOIDMUSMU_DB, createAnnObjs.INPARANOIDRATNO_DB, createAnnObjs.INPARANOIDDROME_DB, createAnnObjs.INPARANOIDSACCE_DB, createAnnObjs.PFAM_DB, createAnnObjs.AFFYHUEX_DB, loadAnnDbPkgIndex, checkMAPCOUNTS, make_eg_to_go_map, make_go_to_eg_map, toSQLStringSet, popHUMANCHIPDB, popHUMANDB, popMOUSECHIPDB, popMOUSEDB, popRATCHIPDB, popRATDB, popARABIDOPSISCHIPDB, popFLYCHIPDB, popFLYDB, popYEASTCHIPDB, popYEASTDB, popMALARIADB, makeHUMANCHIP_DB, makeMOUSECHIP_DB, makeRATCHIP_DB, makeFLYCHIP_DB, makeARABIDOPSISCHIP_DB, makeYEASTCHIP_DB, wrapBaseDBPackages ExportMethods: dbconn, dbfile, dbmeta, dbschema, dbInfo, direction, direction<-, revmap, colnames, colmetanames, Lkeyname, Rkeyname, keyname, tagname, Rattribnames, Rattribnames<-, Lkeys, Rkeys, keys, Lkeys<-, Rkeys<-, keys<-, subset, [, Llength, Rlength, length, isNA, mappedLkeys, mappedRkeys, mappedkeys, count.mappedLkeys, count.mappedRkeys, count.mappedkeys, show, summary, toTable, head, tail, nrow, links, count.links, nhit, ncol, dim, GOID, Term, Ontology, Synonym, Secondary, Definition, as.list, as.character, ls, mget, eapply, get, exists, [[, $, contents, sample, initialize, makeAnnDbPkg ExportClasses: Bimap, FlatBimap, AnnDbObj, L2Rlink, AnnDbBimap, GoAnnDbBimap, Go3AnnDbBimap, GOTermsAnnDbBimap, AnnDbMap, IpiAnnDbMap, AgiAnnDbMap, GOTerms, AnnDbPkgSeed Package: BCRANK Exports: bcrank ExportMethods: show, toptable, fname, searchPath, pwm, plot, bcrankScore, consensus, matchVector ExportClasses: BCRANKmatch, BCRANKsearch, BCRANKresult Package: BGmix Exports: BGmix, ccSummary, ccTrace, ccParams, ccPred, plotCompare, plotBasic, plotTrace, plotFDR, plotPredChecks, plotMixDensity, calcFDR, TailPP, histTailPP, FDRforTailPP, FDRplotTailPP, EstimatePi0, readBGX Package: BSgenome Exports: available.genomes, getSeq, BSgenome, injectSNPs, available.SNPs, forgeSeqFiles, forgeMaskFiles ExportMethods: names, show, length, [[, $, organism, species, provider, providerVersion, releaseDate, releaseName, sourceUrl, SNPlocs_pkgname, seqnames, mseqnames, unload ExportClasses: BSgenome Package: BioMVCClass ExportMethods: ordering, grLayout, rNames, ordering<-, grLayout<-, rNames<-, incidMat, gTestStat, gsTestStat, expData, descr, incidMat<-, gTestStat<-, gsTestStat<-, expData<-, descr<- ExportClasses: graphModel, exprModel, graphView, heatmapView, GSE, gseModel Package: Biobase Exports: Aggregate, addVigs2WinMenu, anyMissing, as.data.frame.ExpressionSet, assayDataNew, assayDataValidMembers, assayDataElementNames, assayDataElement, assayDataElementReplace, assayDataElement<-, biocReposList, cache, copyEnv, copySubstitute, getObjectSlots, createPackage, df2pD, dumpPackTxt, esApply, getPkgVigs, isUnique, l2e, listLen, matchpt, mkScalar, multiassign, note, openPDF, openVignette, package.version, reverseSplit, rowMax, rowMedians, rowMin, rowQ, read.exprSet, read.phenoData, read.pD, readExpressionSet, read.AnnotatedDataFrame, read.MIAME, selectSome, strbreak, subListExtract, testBioCConnection, lcSuffix, lcPrefix, lcPrefixC, updateOldESet, updateObjectFromSlots, userQuery, validMsg ExportMethods: [, [[, $, abstract, aggenv, aggfun, annotatedDataFrameFrom, annotation, channel, channelNames, coerce, combine, content, contents, description, dims, eList, experimentData, expinfo, exprs, featureNames, featureData, fData, fvarLabels, fvarMetadata, geneNames, getExpData, hybridizations, initfun, length, locked, makeDataPackage, normControls, notes, otherInfo, pData, phenoData, preproc, sampleNames, samples, se.exprs, selectChannels, storageMode, varLabels, varMetadata, annotation<-, description<-, dimLabels<-, eList<-, experimentData<-, exprs<-, featureNames<-, featureData<-, fData<-, fvarLabels<-, fvarMetadata<-, geneNames<-, notes<-, preproc<-, pData<-, phenoData<-, sampleNames<-, varLabels<-, varMetadata<-, assayData<-, se.exprs<-, storageMode<-, write.exprs, dim, dimLabels, assayData, reporterNames, reporterNames<-, pubMedIds, pubMedIds<-, isVersioned, isCurrent, classVersion, classVersion<-, updateObject, updateObjectTo, initialize, show, Compare ExportClasses: aggregator, container, eSet, phenoData, MIAME, characterORMIAME, annotatedDataset, AssayData, data.frameOrNULL, exprSet, AnnotatedDataFrame, Versions, VersionsNull, Versioned, VersionedBiobase, ExpressionSet, MultiSet, SnpSet, NChannelSet, ScalarObject, ScalarInteger, ScalarNumeric, ScalarCharacter Package: BiocCaseStudies Exports: parseLibVers, requiredPackages, packages2install, resample, mySessionInfo, fixedWidthCat, lcol1, lcol2, lcol3, dcol1, dcol2, dcol3, numName, sepInt Package: Biostrings Exports: IRanges, intToRanges, intToAdjacentRanges, shift, restrict, narrow, reduce, toNormalIRanges, gaps, Mask, read.gapMask, read.agpMask, read.liftMask, read.rmMask, read.trfMask, readFASTA, writeFASTA, gregexpr2, IUPAC_CODE_MAP, mergeIUPACLetters, AMINO_ACID_CODE, GENETIC_CODE, DNA_ALPHABET, RNA_ALPHABET, AA_ALPHABET, BString, DNAString, RNAString, AAString, BStringSet, DNAStringSet, RNAStringSet, AAStringSet, views, adjacentViews, trim, subviews, mask, FASTArecordsToCharacter, CharacterToFASTArecords, FASTArecordsToXStringViews, XStringSetToFASTArecords, read.XStringViews, read.BStringSet, read.DNAStringSet, read.RNAStringSet, read.AAStringSet, write.XStringSet, write.XStringViews, subXString, subviews, strrev, mkAllStrings, dinucleotideFrequency, trinucleotideFrequency, transcribe, cDNA, dna2rna, rna2dna, .inplaceReplaceLetterAtLoc, maxWeights, maxScore, PWMscore, matchPWM, countPWM, extractAllMatches, alignScore, desc, desc<-, subBString, FASTArecordsToBStringViews, read.BStringViews, write.BStringViews, matchDNAPattern ExportMethods: initialize, length, names, [, [[, show, ==, !=, duplicated, coerce, as.data.frame, as.matrix, as.list, as.character, toString, as.complex, toComplex, nchar, update, start, width, end, isNormal, whichFirstNotNormal, isEmpty, max, min, start<-, width<-, end<-, nir_list, active, active<-, maskedwidth, maskedratio, append, ls, XString, alphabet, subseq, XStringViews, subject, BStringList, DNAStringList, RNAStringList, AAStringList, unmasked, masks, masks<-, letter, substr, substring, alphabetFrequency, oligonucleotideFrequency, chartr, reverse, complement, reverseComplement, replaceLetterAtLoc, maskMotif, injectHardMask, nmismatchStartingAt, nmismatchEndingAt, isMatching, mismatch, coverage, matchPattern, countPattern, vcountPattern, matchLRPatterns, matchProbePair, findPalindromes, palindromeArmLength, palindromeLeftArm, palindromeRightArm, findComplementedPalindromes, complementedPalindromeArmLength, complementedPalindromeLeftArm, complementedPalindromeRightArm, patternFrequency, head, tail, startIndex, endIndex, countIndex, unlist, PDict, matchPDict, countPDict, subpatterns, pattern, align1, align2, type, score, consmat, lcprefix, lcsuffix, pmatchPattern, lcsubstr, pairwiseAlignment, needwunsQS, first, last, BStringViews ExportClasses: IRanges, UnlockedIRanges, Views, LockedIRanges, NormalIRanges, MaskCollection, SparseList, XRaw, XInteger, XString, BString, DNAString, RNAString, AAString, MaskedXString, MaskedBString, MaskedDNAString, MaskedRNAString, MaskedAAString, XStringViews, XStringSet, BStringSet, DNAStringSet, RNAStringSet, AAStringSet, BStringList, DNAStringList, RNAStringList, AAStringList, XStringPartialMatches, XStringAlign, BOC_SubjectString, BOC2_SubjectString, ACtree, Dups, PDict, CWdna_PDict, TBdna_PDict, MIndex, ByPos_MIndex, ByName_MIndex Package: BufferedMatrix ExportMethods: buffer.dim, is.ColMode, is.RowMode, RowMode, ColMode, set.buffer.dim, prefix, directory, filenames, duplicate, ewApply, pow, Max, Min, Sum, Var, Sd, rowMeans, rowSums, rowVars, rowSd, rowMax, rowMin, rowMedians, colMeans, colSums, colVars, colSd, colMax, colMin, colMedians, colRanges, colApply, rowApply, subBufferedMatrix, rownames, colnames, colnames<-, rownames<-, ReadOnlyMode, is.ReadOnlyMode, memory.usage, disk.usage, AddColumn, MoveStorageDirectory, coerce, [, show, as.matrix, ncol, nrow, mean ExportClasses: BufferedMatrix Package: BufferedMatrixMethods Exports: bg.correct.BufferedMatrix, normalize.BufferedMatrix.quantiles, BufferedMatrix.read.celfiles, BufferedMatrix.read.probematrix, BufferedMatrix.justRMA, BufferedMatrix.bg.correct.normalize.quantiles ExportMethods: median.polish.summarize Package: CGHcall ExportMethods: initialize, chromosomes, bpstart, bpend ExportClasses: cghRaw, cghSeg, cghCall Package: Category Exports: .doHyperGTest, applyByCategory, cateGOry, cb_children, cb_contingency, cb_parse_band_Hs, cb_parse_band_Mm, cb_sigBands, cb_test, chrBandInciMat, ChrBandTreeFromGraph, DatPkgFactory, exampleLevels, findAMstats, geneGoHyperGeoTest, geneKeggHyperGeoTest, getPathNames, gseattperm, makeChrBandGraph, makeChrBandInciMat, makeEBcontr, NewChrBandTree, MAPAmat, probes2MAP, probes2Path, ttperm ExportMethods: hyperGTest, linearMTest, universeBuilder, categoryToEntrezBuilder, categoryName, makeValidParams, chrGraph, pvalues, effectSize, geneCounts, universeCounts, universeMappedCount, geneMappedCount, annotation, annotation<-, geneIds, geneIds<-, geneIdsByCategory, geneIdUniverse, condGeneIdUniverse, testName, pvalueCutoff, pvalueCutoff<-, testDirection, testDirection<-, description, universeGeneIds, ontology, ontology<-, conditional, conditional<-, isConditional, oddsRatios, expectedCounts, htmlReport, sigCategories, ID2GO, ID2EntrezID, GO2AllProbes, initialize, show, summary, allGeneIds, childrenOf, level2nodes, lgeneIds, parentOf, treeLevels ExportClasses: DatPkg, AffyDatPkg, YeastDatPkg, OrganismMappingDatPkg, Org.XX.egDatPkg, HyperGParams, GOHyperGParams, KEGGHyperGParams, PFAMHyperGParams, ChrMapHyperGParams, HyperGResultBase, HyperGResult, ChrMapHyperGResult, ChrBandTree, KEGGHyperGResult, PFAMHyperGResult, LinearMParams, ChrMapLinearMParams, LinearMResultBase, LinearMResult, ChrMapLinearMResult Package: CoCiteStats Exports: actorAdjTable, gene.geneslist.sig, gene.geneslist.statistic, gene.gene.statistic, paperLen, twowayTable, twTStats Package: DynDoc Exports: baseVigDesc, editVignetteCode, getPkgVigList, getVigInfo, getVigInfoNames, getVignette, getVignetteCode, getVignetteHeader, hasVigHeaderField, tangleToR, tangleToRFinish, tangleToRRuncode, tangleToRSetup, .transformNames, transformVigInfoLine ExportMethods: chunk<-, chunk, chunkList, chunkName, chunks, codeChunk, codeChunks, evalChunk, evalEnv, getAllCodeChunks, getChunk, getDepends, getKeywords, getOptions, getRequires, getSuggests, indexEntry, numChunks, numOptions, path, pdfPath, setChunk<-, show, summary, SweaveOptions, vigPackage, vigPkgVersion ExportClasses: chunkList, codeChunk, DynDoc, SweaveOptions, Vignette, vignetteCode Package: EBImage Exports: Image, is.Image, stopIfNotImage, display, TrueColor, Grayscale, morphKern, print.Image, print.IndexedImage, median.Image, drawfont, readImage, chooseImage, rgbImage, mkball, mkbox, channelMix, read.image, choose.image ExportMethods: copy, animate, header, assert, combine, tile, untile, writeImage, show, [, channel, as.Image, Arith, colorMode, colorMode<-, fileName, fileName<-, compression, compression<-, resolution, resolution<-, imageData, imageData<-, blur, gblur, contrast, denoise, despeckle, edge, enhance, equalize, cgamma, mediansmooth, noise, resize, rotate, resample, segment, filter2, sharpen2, sharpen, umask, thresh, athresh, cthresh, affinet, modulate, negate, normalize, normalize2, flip, flop, erode, dilate, opening, closing, distmap, watershed, paintObjects, matchObjects, stackObjects, rmObjects, reenumerate, propagate, image, show, hist, cmoments, smoments, rmoments, moments, floodFill, fillHull, frameDist, drawtext, features, getFeatures, hullFeatures, edgeProfile, edgeFeatures, haralickMatrix, haralickFeatures, zernikeMoments, write.image, hull.features, edge.profile, edge.features, haralick.matrix, haralick.features, zernike.moments ExportClasses: Image, IndexedImage Package: GEOquery Exports: parseGEO, parseGSM, parseGSE, parseGDS, parseGPL, getGEO, GDS2MA, GDS2eSet, getGEOfile, gunzip, getGEOSuppFiles ExportMethods: Meta, Columns, GPLList, GSMList, Table, dataTable, Accession, show ExportClasses: GDS, GEODataTable, GEOData, GSE, GPL, GSM, GDS Package: GGBase Exports: snpID ExportMethods: chrnum, rsNum, genesym, show, show, initialize, smList, smlEnv ExportClasses: smlSet, gwSnpScreenResult, multiGwSnpScreenResult, chrnum, rsNum, cnumOrMissing, genesym, cwSnpScreenResult, snpLocNCref, snpMeta, snpMetaWhole, snpID, exFeatID, genesym, snpScreenResult, twSnpScreenResult, racExSet, GGfitter, oGtypeExSet Package: GGtools Exports: HMworkflow, thinHM2rac, exclMono, thinHM2meta, getRare, genoStrings, snps3PrimeTo, snps5PrimeTo, snpsNear, Strains2rac, wrapSNPmetaWh, INBREDSworkflow, addAnno, tx_rsnum, getSNPindices, countRare, make_racExSet, plot_mlp, fastAGMfitter, fastHETfitter ExportMethods: show, plot, topSnps, [, getAbsSnpLocs, initialize, oneFit, snps, exprs, racAssays, snpNames, SNPalleles, snpScreen, twSnpScreen, imputeSNPFixed, nsamp, sampleNames, getSnpLocs, gwSnpScreen, getSnpChroms, getAlleles, plot_EvG, getSnpData, dim, pos, chromosome, updateObject, rawSNP, annotation Package: GOstats Exports: combGOGraph, compCorrGraph, compGdist, enumPairs, GOGraph, GOLeaves, idx2dimnames, isTriad, makeGOGraph, notConn, oneGOGraph, reduce2Degreek, shortestPath, simLL, simLP, simUI, triadCensus, hyperGtable, hyperG2Affy, GOHyperG, probeSetSummary, termGraphs, inducedTermGraph, plotGOTermGraph, selectedGenes ExportMethods: hyperGTest, getGoGraph, pvalues, isConditional, description, oddsRatios, expectedCounts, htmlReport, goDag, geneCounts, universeCounts, geneIds, geneIdUniverse, condGeneIdUniverse, universeMappedCount, geneMappedCount, annotation, testName, summary ExportClasses: GOHyperGResult Package: GSEABase Exports: NullIdentifier, EnzymeIdentifier, GenenameIdentifier, RefseqIdentifier, SymbolIdentifier, UnigeneIdentifier, EntrezIdentifier, AnnotationIdentifier, NullCollection, ExpressionSetCollection, ComputedCollection, KEGGCollection, OMIMCollection, PMIDCollection, ChrCollection, ChrlocCollection, MapCollection, PfamCollection, PrositeCollection, GOCollection, OBOCollection, BroadCollection, asBroadUri, getBroadSets, toBroadXML, getOBOCollection ExportMethods: show, coerce, details, initialize, intersect, union, setdiff, &, |, Logic, incidence, mapIdentifiers, annotation, annotation<-, ids, bcCategory, bcSubCategory, evidenceCode, ontology, subsets, goSlim, GeneSet, geneIdType, geneIds, setIdentifier, setName, description, longDescription, organism, pubMedIds, urls, contributor, setVersion, creationDate, collectionType, geneIdType<-, geneIds<-, setIdentifier<-, setName<-, description<-, longDescription<-, organism<-, pubMedIds<-, urls<-, contributor<-, setVersion<-, creationDate<-, collectionType<-, GeneColorSet, phenotype, geneColor, phenotypeColor, coloring, phenotype<-, geneColor<-, phenotypeColor<-, coloring<-, GeneSetCollection, updateObject, names, [, [[ ExportClasses: GeneIdentifierType, NullIdentifier, AnnotationIdentifier, EntrezIdentifier, EnzymeIdentifier, GenenameIdentifier, RefseqIdentifier, SymbolIdentifier, EntrezIdentifier, UnigeneIdentifier, CollectionType, NullCollection, ExpressionSetCollection, ComputedCollection, CollectionIdType, KEGGCollection, OMIMCollection, PMIDCollection, ChrCollection, ChrlocCollection, MapCollection, PfamCollection, PrositeCollection, GOCollection, OBOCollection, BroadCollection, GeneSet, GeneColorSet, GeneSetCollection Package: GSEAlm Exports: lmPerGene, gsealmPerm, resplot, restrip, CooksDPerGene, dfbetasPerGene, dffitsPerGene, Leverage, getResidPerGene, mnDiffPlot, GSNormalize, identity, one Package: GeneMeta Exports: CountPlot, dstar, f.Q, IDRplot, multExpFDR, mu.tau2, sigmad, tau2.DL, var.tau2, zScoreFDR, zScorePermuted, zScores ExportMethods: getdF Package: GeneR Exports: .seqSize, nSeq, .paramFromIndex, as.segSet, or.segSet, Xor.segSet, not.segSet, and.segSet, plot.segSet, as.data.frame.segSet, as.matrix.segSet, as.globalSeg, or.globalSeg, Xor.globalSeg, not.globalSeg, and.globalSeg, size.globalSeg, Length.globalSeg, Max.globalSeg, Min.globalSeg, as.matrix.globalSeg, plot.globalSeg, range.globalSeg, plot.profile, and.default, or.default, Xor.default, not.default, size.default, Min.default, Max.default, Length.default, insertSeq, strComp, strCompoSeq, placeString, revComp, getSeq, exactWord, dnaToRna, rnaToDna, assemble, concat, compoSeq, appendSeq, bankDensityProfile, densityProfile, freeSeq, freeAllSeq, sizeSeq, sliceSegment, seqSkew, GCcontent, setStrand, getStrand, setBegSeq, getBegSeq, setSeqSize, getSeqSize, getEndSeq, setAccn, getAccn, setParam, getParam, RtoA, AtoT, TtoA, RtoT, TtoR, AtoR, indexFasta, indexGbk, indexEmbl, makeIndex, deleteCR, posMaskedSeqFile, posMaskedSeq, upperSeq, lowerSeq, getOrfs, maxOrf, strTranslate, translate, showTable, readEmblLocation, readGbkLocation, readSeq, sizeSeqEmbl, sizeSeqGbk, sizeSeqFasta, fastaDescription, readFasta, readGbk, readEmbl, randomSeq, shuffleSeq, strReadEmbl, strReadGbk, strReadFasta, or, Xor, and, not, size, Min, Max, Length, .minimalSeg, relist, relistage, xorRecouvr, seqSrs, seqNcbi, writeEmblLine, writeEmblComment, writeEmblSeq, writeFasta, strWriteFasta, mask, unionSeg, bankSummary, readEmblDescript, .transf.limites, Match Package: GeneRfold Exports: fold, dotPlot, rnaPlot Package: GeneSelector Exports: RecoveryScore, AdjustPvalues, GetAlpha, samplingcontrol, HeatmapMethods, GeneSelector, PCAMethods ExportMethods: show, summary, toplist, plot, join, SelectedGenes, GeneInfoScreen, RankingBaldiLong, RankingBstat, RankingEbam, RankingFC, RankingFoxDimmic, RankingGap, RankingLimma, RankingPermutation, RankingSam, RankingShrinkageT, RankingSoftthresholdT, RankingTstat, RankingWelchT, RankingWilcEbam, RankingWilcoxon, GenerateFoldMatrix, GenerateBootMatrix, GetRepeatRanking, GetStabilityLm, GetStabilityOverlap, AggregateBayes, AggregateSimple, variance, AggregatePenalty, AggregatePCA, GetStabilityPCA, GetStabilityGLM ExportClasses: GeneRanking, FoldMatrix, BootMatrix, RepeatRanking, StabilityLm, StabilityOverlap, AggregatedRanking, CombinedRanking, StabilityGLM, PCAMethodsResult, StabilityPCA Package: GeneticsBase Exports: LD, LDband, LDdist, as.geneSet, alleleCount, alleleLevels, alleles, alleleSummary, binsearch, callCodes, callCodes<-, carrier, convert, decodeCallCodes, description, description<-, desMarkers, diseq.inner, diseq.ci, dominant, ci.balance, errorMetrics, errorMetrics<-, extractAlleles, founderGeneSet, geneSet, genotypeFileFormats, genotypeLevels, genotypes, genotypeSummary, gregorius, haplo.score.w, haplo.score.slide.w, haplo.em.w, haplo.scan.w, head, HWE, HWE.chisq, HWE.exact, Armitage, Armitage.default, ArmitageTest, genotypeCoding, genotypeCoding.default, heterozygote, homozygote, html, html.GeneticsBaseSummary, html.markerSummary, html.LD, latex, latex.GeneticsBaseSummary, latex.markerSummary, latex.LD, LDView, left, makeMarkerInfo, makeTransTable, makeTransTableList, markerFileFormats, markerInfo, markerInfo<-, markerNames, markerSummary, missingCodes, missingCodes<-, nallele, nmarker, nobs, notes, notes<-, ped2geneSet, geneSet2Ped, PGtables, phase, phase<-, phenotypeFileFormats, ploidy, ploidy<-, print.GeneticsBaseSummary, print.markerSummary, read.fbat.phe, read.pbat.phe, read.phe, readGenes, readGenes.fbat.ped, readGenes.hapmap.ped, readGenes.pbat.ped, readGenes.ped, readGenes.perlegen, readGenes.pfizer, read.pfizer.Listing, read.pfizer.Pivot, recessive, right, sampleInfo, sampleInfo<-, studyInfo, studyInfo<-, summary.LD, tail, transTables, transTables<-, txt, txt.default ExportMethods: head, html, latex, left, plot, right, show, tail, LD, LDband, LDdist, [, [[, alleleCount, alleleLevels, alleles, callCodes, callCodes<-, carrier, description, description<-, dominant, errorMetrics, errorMetrics<-, genotypeLevels, genotypes, head, heterozygote, homozygote, HWE, markerInfo, markerInfo<-, markerNames, missingCodes, missingCodes<-, nallele, nmarker, nobs, notes, notes<-, phase, phase<-, ploidy, ploidy<-, plot, recessive, sampleInfo, sampleInfo<-, show, studyInfo, studyInfo<-, tail, transTables, transTables<- ExportClasses: LD, LDband, LDdist, geneSet Package: GeneticsDesign Exports: gregorius, power.casectrl, power.genotype.conti, simu.genotype.conti, GeneticPower.Quantitative.Factor, GeneticPower.Quantitative.Numeric, GPC, GPC.default Package: GeneticsPed Exports: Pedigree, as.Pedigree, is.Pedigree, generatePedigree, check, checkId, extend, family, family<-, generation, generation<-, geneContribution, isFounder, nIndividual, prune, removeIndividual, summary.Pedigree, geneFlowT, geneFlowTinv, gameteFlowM, kinship, mendelianSamplingD, inbreeding, inverseAdditive, relationshipAdditive, gpi, gpLong2Wide, hwp Package: GenomeGraphs Exports: gdPlot, DisplayPars ExportMethods: initialize, show, setPar, getPar, drawGD ExportClasses: DisplayPars, GenericArray, MappedRead, BaseTrack, Legend, Title, Gene, Transcript, GeneModel, GenomeAxis, ExonArray, GeneRegion, TranscriptRegion, Ideogram, Segmentation, gdObject, HighlightRegion Package: GlobalAncova Exports: GAGO, GlobalAncova.decomp, pair.compare, Plot.sequential, Plot.all ExportMethods: GlobalAncova, GlobalAncova.closed, Plot.genes, Plot.subjects Package: GraphAlignment Exports: LinearAssignment, ComputeM, AlignNetworks, CreateScoreMatrix, InvertPermutation, Permute, Trace, InitialAlignment, GetBinNumber, VectorToBin, MatrixToBin, ComputeScores, GenerateExample, ComputeLinkParameters, ComputeNodeParameters, EncodeDirectedGraph, AnalyzeAlignment, AlignedPairs, .Last.lib Package: Icens Exports: Bisect, BVcliques, BVclmat, BVmacprod, BVsupport, EM, EMICM, EMICMmac, Intersection, ISDM, Maclist, Macmat, MLEintvl, PGM, Plotboxes, PMGA, rescaleP, Subset, VEM, VEMICMmac Package: KEGGSOAP Exports: color.pathway.by.objects, get.best.best.neighbors.by.gene, getBestNeighbors, get.best.neighbors.by.gene, get.compounds.by.pathway, get.enzymes.by.pathway, get.genes.by.motifs, get.genes.by.organism, get.genes.by.pathway, get.motifs.by.gene, get.paralogs.by.gene, get.pathways.by.compounds, get.pathways.by.enzymes, get.pathways.by.genes, get.pathways.by.reactions, get.reactions.by.pathway, list.databases, list.organisms, list.pathways, mark.pathway.by.objects, search.compounds.by.name, search.glycans.by.name, search.compounds.by.composition, search.glycans.by.composition, search.glycans.by.mass, search.compounds.by.mass, search.compounds.by.subcomp, search.glycans.by.kcam, bget Package: MLInterfaces Exports: tellMLearnMethods, randomForestI, knnI, dldaI, nnetI, rpartI, ldaI, svmI, ldaI.predParms, qdaI, glmI.logistic, RABI, lvqI, naiveBayesI, baggingI, knn2, dlda2, rab, lvq, RAB, DAB, balKfold, xvalSpec, getVarImp, balKfold.xvspec, rdacvI, rdacvML, rdaI, rdaML, plotXvalRDA, makeLearnerSchema, standardMLIConverter, sldaI, Kfold, fs.absT, fs.probT, ksvmI, knn.cvI, knn.cv2, adaI, fs.topVariance ExportMethods: ldaB, qdaB, isoMDSB, knnB, knn1B, lvq1B, lvq2B, lvq3B, olvq1B, agnesB, claraB, dianaB, fannyB, pamB, bclustB, cmeansB, cshellB, lcaB, naiveBayesB, svmB, baggingB, ipredknnB, sldaB, randomForestB, nnetB, pamrB, rpartB, stat.diag.daB, somB, SOMB, hclustB, kmeansB, silhouetteB, gbmB, show, RObject, distMat, predLabels, predLabelsTr, allClass, trainInds, confuMat, confuMatTrain, MLearn, getGrid, planarPlot, Predict, getVarImp, plot, xval, xvalLoop, trainPredictions, xvalML, testScores, testPredictions, fsHistory, report ExportClasses: MLOutput, classifOutput, clustOutput, MLScore, probMat, probArray, membMat, qualScore, silhouetteVec, MLLabel, predClass, groupIndex, varImpStruct, raboostCont, daboostCont, somout, SOMBout, classifierOutput, learnerSchema, nonstandardLearnerSchema, xvalSpec Package: MVCClass ExportMethods: callFun, shortName, preprocessFun, from, childUpdateDataMessage, parentUpdateDataMessage, childName, type, mData, dataName, handleMessage, modelData, modelName, linkData, virtualData, updateModel, provideInfo, modelVar, model, viewList, controller, parentMVC, childMVCList, win, winNum, plotDevice, plotPar, drArea, dfRows, xvar, yvar, clist, motionEvent, clickEvent, identifyView, updateView, redrawView, xval, yval, callFun<-, shortName<-, preprocessFun<-, from<-, childUpdateDataMessage<-, parentUpdateDataMessage<-, childName<-, type<-, mData<-, dataName<-, modelVar<-, modelData<-, modelName<-, linkData<-, virtualData<-, model<-, viewList<-, controller<-, parentMVC<-, childMVCList<-, win<-, winNum<-, plotDevice<-, plotPar<-, drArea<-, dfRows<-, xvar<-, yvar<-, clist<-, xval<-, yval<- ExportClasses: gEventFun, gAddDataMessage, gAddViewMessage, gUpdateDataMessage, gUpdateViewMessage, gAddChildMessage, gSendParentMessage, gSendChildMessage, gMessage, gModifyMessage, gAddMessage, gUpdateMessage, dfModel, gModel, MVC, singleModelMVC, linkedModelMVC, plotView, sPlotView, spreadView, genView, gAskAncestorMessage, qqPlotView Package: MassSpecWavelet Exports: cwt, getLocalMaximumCWT, getRidge, getRidgeLength, identifyMajorPeaks, localMaximum, peakDetectionCWT, plotLocalMax, plotPeak, plotRidgeList, tuneInPeakInfo Package: MeasurementError.cor Exports: cor.me.vector, cor.me.matrix Package: MergeMaid Exports: mergeExprs ExportMethods: exprs, geneNames, names, notes, phenoData, length, show, summary, geneStudy, coeff, stdcoeff, zscore, pairwise.cors, maxcors, integrative.cors, modelOutcome, intCor, plot, hist, intcorDens, intersection, exprs<-, geneNames<-, names<-, notes<-, phenoData<-, geneStudy<-, coeff<-, stdcoeff<-, zscore<- ExportClasses: mergeExpressionSet, mergeCor, mergeCoeff Package: Mfuzz Exports: acore, cselection, cselection, fill.NA, filter.NA, filter.std, filter.std, kmeans2, kmeans2.plot, mfuzz, mfuzz.plot, mfuzz.plot2, mfuzzColorBar, overlap, overlap.plot, partcoef, randomise, standardise, standardise2, top.count Package: OutlierD Exports: OutlierD Package: PCpheno Exports: graphTheory, overlap, complexStatus, buildFDMat, getFDgene, reduceM, densityEstimate, truncName, getDescr, KEGG2SCISI, ppiInteract ExportMethods: hyperGTest, summary, geneCounts, universeCounts, pvalues, oddsRatios, expectedCounts, universeBuilder, categoryToEntrezBuilder, plot ExportClasses: CoHyperGParams, CoHyperGResult, testResult, deResult, gtResult Package: PGSEA Exports: .rwb ExportClasses: smc Package: PROcess Exports: bslnoff, isPeak, pk2bmkr, getMzs, lnn, quality, sigma, getPeaks, noise, read.files, specZoom, intg, peaks, rmBaseline, renorm, binning, gelmap, aveSpec, align, getPeaks2, avesd, is.multiple Package: RBGL Exports: articulationPoints, astarSearch, aver.wavefront, bandwidth, bellman.ford.sp, betweenness.centrality.clustering, biConnComp, brandes.betweenness.centrality, circle.layout, circleLayout, clusteringCoef, clusteringCoefAppr, connectedComp, cuthill.mckee.ordering, dag.sp, dijkstra.sp, dominatorTree, edgeConnectivity, edmunds.karp.max.flow, extractPath, floyd.warshall.all.pairs.sp, fruchtermanReingoldForceDirectedLayout, graphGenerator, gursoyAtunLayout, highlyConnSG, init.incremental.components, incremental.components, is.triangulated, ith.wavefront, isomorphism, johnson.all.pairs.sp, kamada.kawai.spring.layout, kamadaKawaiSpringLayout, kCores, kCliques, kingOrdering, lambdaSets, maxClique, maxWavefront, minCut, minDegreeOrdering, mstree.kruskal, mstree.prim, prim.minST, gprofile, push.relabel.max.flow, randomGraphLayout, removeSelfLoops, rms.wavefront, same.component, separates, sequential.vertex.coloring, sloan.ordering, sp.between, sp.between.scalar, strongComp, transitive.closure, transitivity, tsort ExportMethods: bfs, dfs Package: RBioinf Exports: simpleSort, simpleRand, asSimpleVector, Rcal, subClassNames, superClassNames, simplePVect, LPO, superClasses, class2Graph, S4Help, computeClassLinearization, randDNA, subsetAsCharacter, setVNames, convertMode, printWithNumbers, classList2Graph Package: ROC Exports: AUC, AUCi, dxrule.sca, pAUC, pAUCi, ROC, rocdemo.sca, trapezint ExportMethods: plot, points, lines ExportClasses: rocc Package: RSNPper Exports: .SNPperBaseURL, dot, geneInfo, geneLayout, geneSNPs, ginfoHandler, ginrangeHandler, glayHandler, itemsInRange, nsnpHandler, outPaste, sinrangeHandler, SNPinfo, snpinfoHandler, useSNPper, useSNPper2, doSnpinfo, doGeneinfo ExportMethods: show, geneDetails, popDetails, submitters, toolInfo, allGeneMeta ExportClasses: SNPperMeta, SNPperGeneMeta, fromSNPper Package: RWebServices Exports: createMap, generateDataMap, generateDataTest, generateFunctionMap, regAddonCvt, regAddonCvt2, regTestCvt, printLookup, checkJava2R, reflectObj, checkPkgVersion, cvtCharacterFromJava, cvtCharacterToJava, matchCharacterToJava, cvtIntegerFromJava, cvtIntegerToJava, matchIntegerToJava, cvtLogicalFromJava, cvtLogicalToJava, matchLogicalToJava, cvtNumericFromJava, cvtNumericToJava, matchNumericToJava, cvtRawFromJava, cvtRawToJava, matchRawToJava, cvtComplexFromJava, cvtComplexToJava, matchComplexToJava, cvtVectorFromJava, cvtVectorToJava, matchVectorToJava, cvtListFromJava, cvtListToJava, matchListToJava, cvtArrayFromJava, cvtArrayToJava, matchArrayToJava, cvtMatrixFromJava, cvtMatrixToJava, matchMatrixToJava, cvtFactorFromJava, cvtFactorToJava, matchFactorToJava, cvtDataFrameFromJava, cvtDataFrameToJava, matchDataFrameToJava, cvtEnvFromJava, cvtEnvToJava, matchEnvToJava, cvtUnknownFromJava, cvtUnknownToJava, matchUnknownToJava, cvtCharacterToJava2, matchCharacterToJava2, cvtIntegerToJava2, matchIntegerToJava2, cvtLogicalToJava2, matchLogicalToJava2, 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cvtLogicalMatrixToJava2, matchLogicalMatrixToJava2, cvtRawMatrixFromJava2, cvtRawMatrixToJava2, matchRawMatrixToJava2, cvtComplexMatrixFromJava2, cvtComplexMatrixToJava2, matchComplexMatrixToJava2, cvtEnvFromJava2, cvtEnvToJava2, matchEnvToJava2, unpackAntScript, sinkSetup, sinkRetrieve ExportMethods: typeInfo2Java, show ExportClasses: SinkOutput, RJavaSignature, RJavaPkgFunctions, RawMatrix, CharMatrix, LogicalMatrix, IntegerMatrix, NumericMatrix, ComplexMatrix, RawArray, CharArray, LogicalArray, IntegerArray, NumericArray, ComplexArray Package: Rdbi Exports: dbAppendTable, dbClearResult, dbColumnInfo, dbConnect, dbConnectionInfo, dbDisconnect, dbGetQuery, dbGetResult, dbListTables, dbReadTable, dbReconnect, dbResultInfo, dbSendQuery, dbWriteTable, double.quote, expand.asis, .Last.lib, list.to.csv, list.to.key.pair.string, printListPairs, single.quote, strip.line.feeds Package: RdbiPgSQL Exports: make.db.names, PgSQL, psql, rpgsql.cast.values, rpgsql.cast.values.1042, rpgsql.cast.values.1043, rpgsql.cast.values.1082, rpgsql.cast.values.1083, rpgsql.cast.values.25, rpgsql.cast.values.default, rpgsql.data.type, rpgsql.data.type.dates, rpgsql.data.type.default, rpgsql.data.type.times, rpgsql.format.values, rpgsql.format.values.dates, rpgsql.format.values.default, rpgsql.format.values.times, dbAppendTable Package: Rdisop Exports: addMolecules, decomposeIsotopes, decomposeMass, getMass, getFormula, getIsotope, getValid, getMolecule, getScore, initializeCHNOPS, initializeCHNOPSMgKCaFe, initializeCHNOPSNaK, initializeElements, initializePSE, isotopeScore, RcppVersion, subMolecules Package: Resourcerer Exports: resourcerer2BioC, getResourcerer Package: Rgraphviz Exports: agopen, agread, agwrite, buildEdgeList, buildNodeList, checkAttrs, drawAgNode, drawTxtLabel, getDefaultAttrs, getNodeLabels, getNodeNames, graphvizVersion, graphLayout, makeNodeAttrs, pieGlyph, removedEdges, toFile, agopenSimple, layoutGraph ExportMethods: graphDataDefaults, graphDataDefaults<-, graphData, graphData<-, clusterData, clusterData<-, nodeDataDefaults, nodeDataDefaults<-, nodeData, nodeData<-, edgeDataDefaults, edgeDataDefaults<-, edgeData, edgeData<-, AgEdge<-, AgEdge, AgNode<-, AgNode, agraph, arrowhead, arrowsize, arrowtail, bezierPoints, bLines, botLeft, boundBox, color, cPoints, edgemode, edgeNames, ep, fillcolor, from, getNodeCenter, getNodeHeight, getNodeLW, getNodeRW, getNodeXY, getNodeXY, getPoints, getSpline, getX, getY, head, labelColor, labelFontsize, labelJust, labelLoc, labelText, labelWidth, laidout, layoutType, lines, name, numSplines, plot, pointList, shape, show, sp, splines, style, tail, to, toDot, txtLabel, upRight, renderGraph ExportClasses: AgEdge, AgNode, AgTextLabel, BezierCurve, boundingBox, pEdge, pNode, Ragraph, xyPoint Package: Ringo Exports: autocor, chipAlongChrom, corPlot, whichCsr, computeRunningMedians, sliding.quantile, findChersOnSmoothed, cherByThreshold, newCher, relateChers, preprocess, nimblegenScale, readNimblegen, asExprSet, as.data.frame.cherList, ftr2xys, compute.gc, posToProbeAnno, validProbeAnno, regionOverlap, features2Probes, sliding.meansd, computeSlidingT, getFeats, upperBoundNull ExportMethods: get, ls, initialize, plot, show, arrayName, chromosomeNames, genome, arrayName<-, genome<-, update, cellType, cellType<- ExportClasses: probeAnno, cher Package: Rintact Exports: iListHandler, eListHandler, psi25interaction, psi25complex, intactXML2Graph, list2Matrix, separateXMLDataByExpt ExportMethods: show, initialize, translateIntactID, interactors, interactions, complexes, bait, prey, organismName, taxId, releaseDate ExportClasses: interactionEntry, complexEntry, intactInteraction, intactComplex, intactGraph, intactHyperGraph Package: Rredland Exports: openRedlWorld, readRDF, restoreBDB, cleanXSDT, getArcsWith, getObjectProperties, getDatatypeProperties, getOWLClasses, getPropertyRange, getOWLProperties, getPropertiesWithDomain, getClassElements, getClassGraph, getOWLSubclasses, nodeFromURIString, world ExportMethods: ref, freeRedl, getStatus, setStatus, makeRedlURI, show, size, coerce, world ExportClasses: redlWorld, redlModel, redlURI, redlNode Package: Rtreemix Exports: Pval.dist, kullback.leibler, L1.dist, cosin.dist, L2.norm, euclidian.dist, rank.cor.dist, get.tree.levels, comp.models, comp.models.levels, comp.trees, comp.trees.levels, stability.sim ExportMethods: initialize, print, show, Sample, Events, Patients, Description, sampleSize, eventsNum, Events<-, Patients<-, Description<-, Weights, Weights<-, WeightsCI, Resp, CompleteMat, Star, Trees, numTrees, getTree, getData, plot, Model, LogLikelihoods, WLikelihoods, getResp, SamplingMode, SamplingParam, GPS, gpsCI, SimPatterns, SamplingTimes, WaitingTimes, getModel, noDraws, fit, bootstrap, likelihoods, gps, confIntGPS, sim, generate, distribution ExportClasses: RtreemixData, RtreemixModel, RtreemixSim, RtreemixStats, RtreemixGPS Package: Ruuid Exports: getuuid ExportMethods: show, as.character, ==, !=, uuid ExportClasses: Ruuid, uuidt Package: SAGx Exports: clin2mim, cluster.q, estimatep0, fetchSignal, firstpass, fom, fp.fn, Fstat, gap, GSEA.mean.t, JT.test, list.experiments, list.intersection.p, mat2TeX, myclus, normalise, one.probeset.per.gene, outlier, p0.mom, pava, pava.fdr, R2BASE, R2mim, rank.genes, rank.trend, rsd.test, samrocN, samrocNboot, union.of.pways, Xprep, Xprep.resid ExportMethods: show, plot ExportClasses: samroc.result Package: SLGI Exports: gi2Interactome, getInteraction, getSharedInteraction, hyperG, comemberIn, congruence, normInteraction, topInteraction, createSquareMatrix, byComplex, domainDist, getSharedDomains, sharedBy, getUniquePairs, getTestedPairs, seqMatcherAlign, getAlignStats, twoWayTable, modelSLGI, getFASTAname, test2Interact, iSummary, withinComplex, sharedInt ExportMethods: plot, compare, show ExportClasses: siResult Package: SMAP Exports: SMAPHMM, SMAPObservations ExportMethods: name, value, noObservations, chromosome, startPosition, endPosition, reporterId, A, Pi, Phi, noStates, HMM, observations, P, Q, smap, initialize, show, plot ExportClasses: SMAPObservations, SMAPHMM, SMAPProfile, SMAPProfiles Package: SNPchip Exports: centromere, chromosome2numeric, chromosomeSize, plotPredictions, showSummary, plotCytoband ExportMethods: $, $<-, plotSnp, snpPar, snpPar<-, initialize, alleleA, alleleB, cnConfidence, cnConfidence<-, ratioConfidence, ratioConfidence<-, coerce, copyNumber, copyNumber<-, dbSnpId, fragmentLength, hmmPredict, selectSomeIndex, show, smoothSnp, summary, updateObject, ratio, ratio<-, snpset ExportClasses: ParESet, ParSnpCopyNumberSet, ParSnpCallSet, ParSnpSet, HmmPredict, RatioSnpSet Package: ScISI Exports: JaccardCoef, ScISI2html, calcGraphStats, checkComplex, checkSGN, compBijection, compareComplex, createGODataFrame, createGOMatrix, createMipsDataFrame, createMipsMatrix, createYeastDataObj, edgeProp, findSubComp, getAPMSData, getGOInfo, getLocOrfs, getMipsInfo, graphSumStats, maximizeSimilarity, meanDeg, mergeBGMat, recCompSize, rmByEvi, runAlignment, runCompareComplex, sumStats, unWantedComp, xtraGONodes ExportMethods: ID, Desc, getURL ExportClasses: yeastData Package: TypeInfo Exports: IndependentTypeSpecification, SimultaneousTypeSpecification, ReturnTypeSpecification, TypedSignature, StrictIsTypeTest, InheritsTypeTest, checkArgs, checkReturnValue, typeInfo, typeInfo<-, paramNames, hasParameterType, hasReturnType ExportMethods: initialize, coerce, checkArgs, showTypeInfo ExportClasses: TypedSignature, NamedTypeTest, InheritsTypeTest, StrictIsTypeTest, DynamicTypeTest, ClassNameOrExpression, TypeSpecification, IndependentTypeSpecification, SimultaneousTypeSpecification, ReturnTypeSpecification Package: VanillaICE Exports: getChromosomeArm, addFeatureData, calculateCnSE, calls.emission, copyNumber.emission, makeTable, scaleTransitionProbability, viterbi ExportMethods: [, annotation, annotation<-, breakpoints, breakpoints<-, calculateBreakpoints, calculateDistance, physicalDistance, calls.ICE, calls.ICE<-, copyNumber.ICE, copyNumber.ICE<-, coerce, db, emission, emission<-, featureNames, hmm, initialize, pData, pi, position, predictions, predictions<-, probHomCall, probHomCall<-, snpset, snpset<-, states, states<-, show, summary, tau, genomicDistance, genomicDistance<-, term5, term5<-, transitionScale, transitionScale<- ExportClasses: HmmParameter, HmmOptions Package: XDE Exports: calculatePosteriorAvg, empiricalStart, ssStatistic, symbolsInteresting, xde, xsScores ExportMethods: [, [[, $, bayesianEffectSize, bayesianEffectSize<-, burnin, burnin<-, calculateBayesianEffectSize, firstMcmc, firstMcmc<-, coerce, directory, directory<-, featureData, featureNames, geneCenter, hyperparameters, hyperparameters<-, initialize, .integrativeCorrelationFilter, iterations, iterations<-, xapply, lastMcmc, lastMcmc<-, notes, nrow, nSamples, output, output<-, pData, phenotypeLabel, phenotypeLabel<-, plot, posteriorAvg, posteriorAvg<-, savedIterations, seed, seed<-, show, showIterations, showIterations<-, .standardizedDelta, standardizeSamples, studyCenter, studyNames, studyNames<-, thin, thin<-, tuning, tuning<-, updates, updates<-, zeroNu ExportClasses: ExpressionSetList, XdeParameter, XdeMcmc Package: adSplit Exports: adSplit, diana2means, drawRandomPS, randomDiana2means, makeEID2PROBESenv Package: affyPara Exports: distributeFiles, removeDistributedFiles, splitAffyBatch, splitFileVector, splitMatrix, file.name, bgCorrectPara, normalizeAffyBatchQuantilesPara, normalizeAffyBatchInvariantsetPara, normalizeAffyBatchConstantPara, computeExprSetPara, preproPara, rmaPara, mergeAffyBatches, combineMatrices Package: affycomp Exports: affycomp, affycomp.compfig2, affycomp.compfig2b, affycomp.compfig3, affycomp.compfig4a, affycomp.compfig4b, affycomp.compfig4c, affycomp.compfig5a, affycomp.compfig5b, affycomp.compfig5c, affycomp.compfig5cde, affycomp.compfig5d, affycomp.compfig5e, affycomp.compfig7, affycomp.compfigs, affycomp.compfigs.calls, affycomp.figure1, affycomp.figure1b, affycomp.figure2, affycomp.figure2b, affycomp.figure3, affycomp.figure4a, affycomp.figure4b, affycomp.figure4c, affycomp.figure5a, affycomp.figure5b, affycomp.figure5c, affycomp.figure5d, affycomp.figure5e, affycomp.figure6a, affycomp.figure6b, affycomp.figure7, affycomp.figure.calls, affycomp.figures, affycompPlot, affycompTable, assessAll, assessDilution, assessFC, assessFC2, assessLS, assessMA, assessMA2, assessSD, assessSignal, assessSpikeIn, assessSpikeIn2, assessSpikeInSD, exprset.log, read.dilution, read.newspikein, read.spikein, remove.hgu133a.xhyb, tableAll, tableDilution, tableFC, tableFC2, tableLS, tableMA2, tableOverallSNR, tableRanks, tableSD, tableSignal, tableSpikeInSD Package: affycoretools Exports: limma2annaffy, foldFilt, vennSelect, vennCounts2, plotma, probes2table, affystart, plotDeg, plotHist, plotPCA, convert.back, hyperG2annaffy, vennSelectBM, limma2biomaRt, linksBM, annBM, foldFiltBM, probes2tableBM, vennSelectFC, hyperGoutput, getUniqueLL Package: annaffy Exports: selectorWidget, is.annpkg ExportMethods: colnames, colnames<-, getCSS, getHTML, getTD, getText, getURL, probeids, probeids<-, saveHTML, saveText, show, [, [[ ExportClasses: aafChromLoc, aafChromosome, aafCytoband, aafDescription, aafGenBank, aafGO, aafGOItem, aafIntensity, aafList, aafLocusLink, aafPathway, aafPathwayItem, aafProbe, aafPubMed, aafSigned, aafSymbol, aafTable, aafUniGene Package: annotate Exports: .buildAnnotateOpts, .getIdTag, .getNcbiURL, .handleXML, .pmfetch, .transformAccession, ACC2homology, accessionToUID, ACCNUMStats, annPkgName, aqListGOIDs, buildChromLocation, buildPubMedAbst, checkArgs, chrCats, compatibleVersions, createLLChrCats, createMAPIncMat, dropECode, filterGOByOntology, findChr4LL, findNeighbors, genbank, genelocator, getAnnMap, getBoundary, getEG, getEvidence, getGI, getGO, getGOChildren, getGOdesc, getGOOntology, getGOParents, getGOTerm, getGPLNames, getLL, getOntology, getOrgNameNCode, getPMID, getPMInfo, getQueryLink, getSAGEFileInfo, getSAGEGPL, getSEQ, getSYMBOL, getUniqAnnItem, getValidChr, GO2heatmap, GOmnplot, hasGOannote, HGID2homology, homoData, htmlpage, KEGG2heatmap, KEGGmnplot, LL2homology, lookUp, makeAnchor, mapOrgs, neighborGeneFinder, p2LL, pm.abstGrep, pm.getabst, pm.titles, pmAbst2HTML, pmid2MIAME, PMIDAmat, pmidQuery, probesByLL, pubmed, PWAmat, readGEOAnn, readIDNAcc, readUrl, serializeDataPkgEnvs, serializeEnv, UniGeneQuery, usedChromGenes, usedChromGenes, weightByConfi, whatACC ExportMethods: abstText, articleTitle, authors, chromInfo, chromLengths, chromLocs, chromNames, dataSource, Definition, fileName, geneSymbols, GOID, homoACC, homoHGID, homoLL, homoOrg, homoPS, homoType, homoURL, initialize, journal, mainPage, nChrom, Ontology, organism, pageText, pageTitle, pmid, probesToChrom, pubDate, pubMedAbst, Secondary, show, sidePage, Synonym, Term, toFile, topPage ExportClasses: chromLocation, FramedHTMLPage, homoData, HTMLPage, pubMedAbst Package: arrayQuality Exports: readAgilent, readcontrolCode, agQuality, EMSplit, getSpikeIds, getSpikeIndex, gpQuality, globalQuality, maQualityPlots, meeboQuality, meeboQualityPlots, heeboQuality, heeboQualityPlots, PRv9mers, PRvQCHyb, qualBoxplot, qualityScore, qcScore, readGPR, readSpikeTypes, readSpot, slideQuality, scaleRefTable, spotQuality, HeeboSpotTypes, MeeboSpotTypes, controlCodeHeebo, controlCodeMeebo Package: arrayQualityMetrics Exports: arrayQualityMetrics, addXYfromGAL Package: beadarray Exports: SAMSummary, BeadChipSummary, medianNormalise, rankInvariantNormalise, plotBeadIntensities, plotBeadLocations, imageplot, plotMAXY, plotMA, plotRG, plotXY, plotOnSAM, readQC, readIllumina, readBeadSummaryData, findBeadStatus, boxplotBeads, createBeadSummaryData, findAllOutliers, qcBeadLevel, plotBeadDensities, beadResids, readBGX, normaliseIllumina, beadarrayUsersGuide ExportMethods: initialize, show, se.exprs, exprs, [, [[, $, phenoData, pData, sampleNames, samples, se.exprs<-, exprs<-, NoBeads<-, Detection<-, QCInfo<-, dim, assayData, initialize, NoBeads, Detection, backgroundCorrect, QCInfo, copyBeadLevelList, combineBeadLevelLists, getProbeIntensities, getArrayData, arrayNames, numBeads, getVariance, combine ExportClasses: ExpressionSetIllumina, BeadLevelList Package: beadarraySNP Exports: read.SnpSetIllumina, backgroundEstimate, backgroundCorrect.SNP, normalizeBetweenAlleles.SNP, normalizeWithinArrays.SNP, normalizeLoci.SNP, RG2polar, polar2RG, standardNormalization, heterozygousSNPs, compareGenotypes, heterozygosity, reportSamplesSmoothCopyNumber, reportChromosomesSmoothCopyNumber, pdfSamplesSmoothCopyNumber, pdfChromosomesSmoothCopyNumber, removeLowQualityProbes, removeLowQualitySamples, calculateQCarray, pdfQC, smoothed.intensity, renameOPA, calculateLOH, reportGenomeGainLossLOH, pdfChromosomeGainLossLOH, reportChromosomeGainLossLOH, reportGenomeIntensityPlot, convert2aCGH, convert2SegList, segmentate, reportGenotypeSegmentation, plotGoldenGate4OPA, createCNSummary, alterCN, getDNAindex, interactiveCNselect, setRealCN, Sample_Map2Samplesheet, pdfBeadstudioQC, BeadstudioQC, calculateLair ExportMethods: [, [[, $, annotation, combine, experimentData, exprs, featureNames, pData, phenoData, sampleNames, samples, featureData, annotation<-, description<-, experimentData<-, exprs<-, featureNames<-, geneNames<-, pData<-, phenoData<-, sampleNames<-, assayData<-, featureData<-, fData, fData<-, dim, assayData, reporterNames, initialize, arrayType<-, arrayID<-, arrayType, arrayID, plotQC, reportSamplePanelQC, calculateGSR ExportClasses: SnpSetIllumina, QCIllumina Package: bgafun Exports: convert_aln_amino, convert_aln_AAP, average_cols_aap, remove_gaps_groups, add_pseudo_counts, run_between_pca, top_residues_2_groups, create_profile_strings, Calculate_Row_Weights Package: bgx Exports: bgx, standalone.bgx, readOutput.bgx, plotExpressionDensity, plotDEDensity, plotDEHistogram, rankByDE, plotDiffRank Package: bioDist Exports: cor.dist, spearman.dist, tau.dist, euc, man, mutualInfo, KLdist.matrix, KLD.matrix, closest.top, MIdist ExportMethods: KLD.matrix, KLdist.matrix, cor.dist, euc, man, mutualInfo, MIdist, spearman.dist, tau.dist Package: biocGraph Exports: imageMap Package: biocViews Exports: writeBiocViews, getBiocViews, write_VIEWS, write_REPOSITORY, genReposControlFiles, extractVignettes, writeRepositoryHtml, writePackageDetailHtml, getSubTerms, getBiocSubViews, writeTopLevelView, writeHtmlDoc, write_SYMBOLS ExportMethods: coerce, show, htmlDoc, htmlValue, htmlFilename ExportClasses: Htmlized, PackageDetail, pdAuthorMaintainerInfo, pdVignetteInfo, pdDownloadInfo, pdDetailsInfo, pdDescriptionInfo, pdVigsAndDownloads, RepositoryDetail, rdPackageTable, BiocView, bvTitle, bvPackageTable, bvSubViews, bvParentViews Package: biomaRt Exports: martDisconnect, listMarts, getGene, getGO, getAffyArrays, getSequence, getSNP, getHomolog, exportFASTA, useMart, listDatasets, useDataset, listAttributes, listFilters, getBM, parseAttributes, parseFilters, getLDS, attributeSummary, filterSummary, filterOptions, filterType ExportMethods: show ExportClasses: Mart Package: bridge Exports: bridge.2samples, bridge.3samples Package: cellHTS Exports: ROC, annotate, Bscore, configure, getEnVisionRawData, getEnVisionCrosstalkCorrectedData, getLibraryPlate, getMatrix, imageScreen, normalizeChannels, normalizePlates, oneRowPerId, plotSpatialEffects, plotPlateLibrary, readPlateData, screenMatch, summarizeChannels, summarizeReplicates, write.tabdel, writeReport, writeTab Package: cellHTS2 Exports: oneRowPerId, Bscore, configurationAsScreenPlot, convertOldCellHTS, convertWellCoordinates, getEnVisionRawData, getEnVisionCrosstalkCorrectedData, getDynamicRange, getMeasureRepAgreement, getTopTable, getZfactor, imageScreen, normalizePlates, plotSpatialEffects, readPlateList, readHTAnalystData, scores2calls, scoreReplicates, spatialNormalization, summarizeChannels, summarizeReplicates, templateDescriptionFile, writeReport, write.tabdel ExportMethods: annotate, batch, batch<-, compare2cellHTS, configure, Data, Data<-, geneAnno, initialize, intensityFiles, lines, meanSdPlot, name, name<-, nbatch, pdim, plate, plateConf, plateEffects, plateList, plot, position, ROC, screenDesc, screenLog, show, state, well, wellAnno, writeTab ExportClasses: cellHTS, ROC Package: cghMCR Exports: cghMCR, plot.DNAcopy, getSegments, MCR, mergeMCRProbes ExportClasses: cghMCR Package: codelink Exports: readCodelink, readCodelink2, writeCodelink, reportCodelink, plotMA, plotCorrelation, plotDensities, plotCV, imageCodelink, bkgdCorrect, normalize, mergeArray, createWeights, arrayNew, selCV, cutCV, fc2Cond, na2false, logCodelink, readCodelink2 ExportMethods: [, show, summary, summaryFlag, annotation, codCorrect, codNormalize, codPreprocess, probeNames, probeTypes, getSNR, getInt, getBkg, getInfo, meanSNR, codPlot, exprs, chipDevice, filterSNR, codUniverse, writeCluster ExportClasses: Codelink, CodelinkSet Package: copa Exports: copa, plotCopa, copaPerm, tableCopa, scatterPlotCopa, summaryCopa Package: cosmo Exports: cosmo, bgModel, bfile2tmat, makeConSet, addCon, makeBoundCon, makePalCon, makeShapeCon, makeShapeDiffCon, makePosFreqCon, makeSubMotifCon, writeConFile, readConFile, rseq, simScore, license.cosmo ExportMethods: plot, summary, print, show ExportClasses: align, intInfo, cosmo, constraintSet, boundCon, palCon, posFreqCon, shapeCon, shapeDiffCon, subMotifCon Package: cosmoGUI Exports: constraintBuilder Package: ctc Exports: hc2Newick, hclust2treeview, r2cdt, r2atr, r2gtr, r2cluster, r2xcluster, read.eisen, xcluster, xcluster2r Package: edd Exports: eddDistList, T3, U01, N01, LN01, B82, CS1, B28, centerScale, dmixnorm, edd, eddObsolete, flatQQNorm, flatQQNormY, fq.matrows, latEDtable, makeCandmat.raw, makeCandmat.theor, maxKSp, mkt, plotED, pmixnorm, qmixnorm, rmixnorm, rmixnorm.alt, MIXN1 ExportMethods: CDFname, genName, latexTag, Mad, med, parms, plotlim, qfName, qfun, stub, tag, testVec ExportClasses: eddDist Package: externalVector Exports: externalCharacter, externalComplex, externalInteger, externalLogical, externalMatrix, externalNumeric, externalVector, makeSlice, nonSlotAttributes, nonSlotAttributes<-, rebind, setExternalStorageClass, setVirtualMethod, SubscriptList ExportMethods: allNA, allocatedSize, allocatedType, allocate, allocator, anyNA, apply, Arith, as.character, as.complex, as.data.frame, asEach, as.integer, as.list, as.logical, as.matrix, as.numeric, as.Rmatrix, as.Rvector, as.single, as.vector, [<-, [, [[<-, [[, c, coerce, colMeans, colSums, Compare, Complex, cor, cov2cor, cov, deallocate, defaultElement, dim<-, dim, dimnames<-, dimnames, external.size<-, external.size, force, getExternalStorage, getNativeStorageMethods, getPointer, initialize, initializeResource, internalType, is.finite, is.infinite, is.na, is.nan, lapply, length<-, length, log, match, Math, mean, median, names<-, names, Ops, reinitializePointer, rowMeans, rowSums, sapply, setDimNames, setNames, show, Subset2, Subset, Summary, var ExportClasses: noneIndex, allIndex, externalAllocator, externalResource, externalStorage, externalVector, externalVectorWithStorage, gcAllocator, indirectExternalMatrix, indirectExternalVector, matrixIndex, NAIndex, nativeStorageMethods, nativeStorageMethodsList, positiveIndex, simpleStorage, sliceIndex, vectorIndex Package: fbat Exports: readPed, readLink, readHapMap, getFounders, fbat, fbat.default, pedHardyWeinberg, pedHardyWeinberg.default, pedFlagHomo, pedFlagHomo.default, pedGFreq, pedGFreq.default, pedAFreq, pedAFreq.default, viewHW, viewstat, viewFlagHomo, summaryPvalue, checkMarkers, checkMarkers.default, checkMendelian, checkMendelian.default, missGFreq, missGFreq.default Package: flowClust ExportMethods: show, summary, plot, density, hist, filter, %in%, [, coerce, coerce<-, Subset, split, ruleOutliers, ruleOutliers<-, Map ExportClasses: flowClust, tmixFilter, tmixFilterResult Package: flowCore Exports: arcsinhTransform, as.data.frame.manyFilterResult, biexponentialTransform, curv1Filter, curv2Filter, ellipsoidGate, expressionFilter, filterReference, filterSet, flowFrame, flowSet, kmeansFilter, linearTransform, lnTransform, logTransform, logicleTransform, manyFilterResult, norm2Filter, polygonGate, polytopeGate, print.filterSummary, quadGate, quadraticTransform, read.FCS, read.FCSheader, read.flowSet, rectangleGate, sampleFilter, scaleTransform, splitScaleTransform, truncateTransform, %&%, %in% ExportMethods: coerce, colnames, colnames<-, compensate, description, description<-, dim, each_row, each_col, exprs, exprs<-, featureNames, filter, filterDetails, filterDetails<-, filterReference, fsApply, head, identifier, identifier<-, keyword, keyword<-, length, names, ncol, nrow, parameters, parameters<-, pData, pData<-, phenoData, phenoData<-, plot, range, rbind2, sampleNames, sampleNames<-, show, sort, spillover, split, Subset, summary, tail, transform, varLabels, varLabels<-, %in%, %on%, %subset%, [, [[, [[<- ExportClasses: complementFilter, concreteFilter, curv1Filter, curv2Filter, ellipsoidGate, expressionFilter, filter, filterReference, filterResult, filterSet, flowFrame, flowSet, intersectFilter, kmeansFilter, logicalFilterResult, manyFilterResult, multipleFilterResult, norm2Filter, parameterFilter, polygonGate, polytopeGate, quadGate, randomFilterResult, rectangleGate, sampleFilter, setOperationFilter, subsetFilter, transform, transformMap, transformList, transformFilter, unionFilter Package: flowQ Exports: validProcess, qaProcess, aggregatorList, qaGraph, qaGraphList, qaProcessFrame, writeQAReport, qaReport, qaProcess.marginevents, qaProcess.timeline, binaryAggregator, discreteAggregator, factorAggregator, stringAggregator, numericAggregator, rangeAggregator, evaluateProcess ExportMethods: outliers, initialize, show, names, writeLines ExportClasses: outlierResult, qaAggregator, binaryAggregator, discreteAggregator, factorAggregator, stringAggregator, numericAggregator, rangeAggregator, aggregatorList, qaGraph, qaGraphList, qaProcessFrame, qaProcess Package: flowUtils Exports: read.gatingML, read.transformML, read.compensationML Package: flowViz Exports: panel.densityplot.flowset, prepanel.densityplot.flowset, panel.ecdfplot.flowset, prepanel.ecdfplot.flowset, prepanel.xyplot.flowset, panel.xyplot.flowset, timeLinePlot ExportMethods: densityplot, xyplot, levelplot, qqmath, plot, splom, parallel, ecdfplot, glines, gpolygon, gpoints, glpoints, glpolygon, flowPlot, timeLinePlot Package: gaga Exports: checkfit, checkfit.gagafit, classpred, classpred.gagafit, dcgamma, findgenes, findgenes.gagafit, fit.gg, getpar, getpar.gagafit, mcgamma, parest, parest.gagafit, print.gagafit, rcgamma, sim.gg, simnewsamples, simnewsamples.gagafit, powclasspred, powclasspred.gagafit Package: gaggle Exports: gaggleInit, getNameList, getCluster, getMatrix, getNetwork, getTuple, broadcast, geese, getTargetGoose, setTargetGoose, setSpecies, getSpecies, showGoose, hideGoose, testGagglePackage, connectToGaggle, disconnectFromGaggle Package: gcrma Exports: average.for.PAV, base.profiles, base.profiles.mm, base.profiles.nc, bg.adjust.affinities, bg.adjust.constant, bg.adjust.fullmodel, bg.adjust.gcrma, bg.adjust.mm, bg.adjust.optical, bg.parameters.ns, check.probes, compute.affinities, compute.affinities.local, compute.affinity.coef, fast.bkg, gcrma, gcrma.bg.transformation, gcrma.bg.transformation.fast, gcrma.engine, gcrma.engine2, getCDF, getProbePackage, just.gcrma, justGCRMA, left.sigma, mem.bkg, PAV, plotBaseProfiles Package: genefilter Exports: Anova, allNA, anyNA, coxfilter, cv, eSetFilter, varFilter, featureFilter, fastT, ttest, shorth, half.range.mode, rowttests, colttests, rowFtests, colFtests, rowSds, rowVars, dist2, filterfun, findLargest, gapFilter, genefilter, genescale, getFilterNames, getFuncDesc, getRdAsText, isESet, kOverA, maxA, pOverA, parseArgs, parseDesc, setESetArgs, showESet ExportMethods: genefinder, show, plot, [, sens, spec, area, pAUC, AUC, rowpAUCs, nsFilter ExportClasses: rowROC Package: geneplotter Exports: alongChrom, cColor, cPlot, cScale, dChip.colors, greenred.colors, GetColor, plotChr, plotExpressionGraph, make.chromOrd, savepng, savepdf, saveeps, savetiff, smoothScatter, densCols, histStack, openHtmlPage, closeHtmlPage, panel.smoothScatter, multiecdf, multidensity ExportMethods: Makesense, imageMap ExportClasses: file, connection Package: globaltest Exports: globaltest, permutations, sampling, geneplot, sampleplot, regressionplot, checkerboard, gt.multtest, mlogit, makeGOstructure, gtGO, getFocus ExportMethods: [, show, result, p.value, length, names, names<-, sort, size, hist, z.score, scale, plot, combine, fit, summary, residuals, fitted.values, coefficients, genesets ExportClasses: gt.result, gt.barplot, mlogit, GOstructure Package: goProfiles Exports: basicProfile, expandedProfile, GOTermsList, getAncestorsLst, getGOLevel, compSummary, equivSummary, fitGOProfile, compareGOProfiles, compareProfilesLists, compareGeneLists, plotProfiles, printProfiles, mergeProfilesLists, as.GOTerms.frame, as.GOTerms.list, BioCpack2EntrezIDS, BioCpack2Profiles, BioCprobes2Entrez, GOTermsFrame2GOTermsList, expandTerm, expandedLevel, equivalentGOProfiles Package: gpls Exports: gpls, glpls1a, glpls1a.cv.error, glpls1a.train.test.error, glpls1a.mlogit, glpls1a.logit.all, glpls1a.mlogit.cv.error Package: graph Exports: boundary, buildRepDepGraph, calcProb, calcSumProb, duplicatedEdges, graph2SparseM, listEdges, randomEGraph, randomGraph, randomNodeGraph, validGraph, eWV, pathWeights, .dropEdges, aveNumEdges, sparseM2Graph, gxlTreeNEL, ftM2adjM, ftM2graphNEL, .ftM2other, int2ftM, ftM2int, aM2bpG, mostEdges, numNoEdges, reverseEdgeDirections, ugraphOld, graph.par, graph.par.get, graphRenderInfo, nodeRenderInfo, edgeRenderInfo, parRenderInfo, nodeRenderInfo<-, edgeRenderInfo<-, parRenderInfo<-, graphRenderInfo<- ExportMethods: DFS, Dist, acc, addEdge, addNode, adj, clearNode, clusteringCoefficient, combineNodes, complement, connComp, degree, dumpGXL, edgeL, edgeMatrix, edgeNames, edgeWeights, edgemode, edgemode<-, edges, nodes<-, fromGXL, inEdges, initialize, intersection, intersection2, isAdjacent, isConnected, isDirected, join, nodes, numNodes, numEdges, removeEdge, removeNode, show, subGraph, threshold, toGXL, union, validateGXL, coerce, toDotR, attrDefaults, attrDefaults<-, edgeDataDefaults, edgeDataDefaults<-, nodeDataDefaults, nodeDataDefaults<-, edgeData, edgeData<-, nodeData, nodeData<-, attrDataItem, attrDataItem<-, removeAttrDataItem<-, ugraph, leaves, updateGraph ExportClasses: distGraph, clusterGraph, graph, graphNEL, file, connection, gzfile, bzfile, url, graphAM, attrData, simpleEdge, edgeSet, edgeSetNEL, edgeSetAM, multiGraph, renderInfo Package: hexbin Exports: erode, erode.hexbin, getHMedian, gplot.hexbin, grid.hexagons, grid.hexlegend, hboxplot, hcell2xy, hexbin, hexcoords, hexList, hexpolygon, hexViewport, hexVP.abline, plotMAhex, hexVP.loess, hexMA.loess, hsmooth, list2hexList, pushHexport, smooth.hexbin, hdiffplot, hcell2xyInt, hgridcent, hexGraphPaper, hexTapply, optShape, inout.hex, BTC, BTY, LinGray, LinOCS, heat.ob, magent, plinrain, panel.hexbinplot, panel.hexboxplot, panel.hexgrid, panel.hexloess, hexbinplot, hexbinplot.formula, hexlegendGrob, hexplom, hexplom.formula, hexplom.data.frame ExportMethods: erode, hsmooth, plot, summary, show, coerce ExportClasses: hexbin, erodebin, smoothbin, hexVP, integer or NULL, hexbinList Package: hypergraph Exports: kCoresHypergraph, vCoverHypergraph, Hypergraph, Hyperedge, DirectedHyperedge, l2hel ExportMethods: nodes, label, label<-, show, toUndirected, head, tail, hyperedges, numNodes, inciMat, initialize, toGraphNEL, hyperedgeLabels ExportClasses: Hypergraph, Hyperedge, DirectedHyperedge Package: idiogram Exports: .usedChromExprs, .rwb ExportClasses: cytoband Package: impute Exports: impute.knn Package: limma ExportMethods: show ExportClasses: RGList, MAList, MArrayLM, TestResults, LargeDataObject Package: logicFS Exports: getMatEval, logic.bagging, logic.oob, logic.pimp, logicFS, make.snp.dummy, minDNF, prime.implicants, vim.chisq, vim.ebam, vim.logicFS, vim.norm, vim.perm, vim.individual, vim.set, contr.none, contr.snps, mlogreg, logic.fs, logic.vim Package: macat Exports: buildMACAT, compute.sliding, loaddatapkg, discreteKernelize, discretize, discretize.tscores, discretizeAll, evalScoring, evaluateParameters, getResults, kernelize, kernelizeAll, kernelizeToPython, preprocessedLoader, scoring, plotSliding, kNN, rbf, basePairDistance, getsteps, kernelmatrix Package: maigesPack Exports: activeMod, activeModScoreHTML, activeNet, activeNetScoreHTML, addGeneGrps, addPaths, bootstrapCor, bootstrapMI, bootstrapT, calcA, calcW, classifyKNN, classifyKNNsc, classifyLDA, classifyLDAsc, classifySVM, classifySVMsc, compCorr, contrastsFitM, createMaigesRaw, createTDMS, deGenes2by2BootT, deGenes2by2Ttest, deGenes2by2Wilcox, deGenesANOVA, designANOVA, getLabels, heatmapsM, hierMde, hierM, kmeansMde, kmeansM, loadData, MI, normLoc, normOLIN, normRepLoess, normScaleLimma, normScaleMarray, plotGenePair, relNet2TGF, relNetworkB, relNetworkM, robustCorr, selSpots, somMde, somM, summarizeReplicates, tableClass, tablesDE ExportMethods: coerce, show, [ ExportClasses: maigesPreRaw, maigesRaw, maiges, maigesANOVA, maigesDE, maigesDEcluster, maigesClass, maigesRelNetM, maigesRelNetB, maigesActMod, maigesActNet Package: makecdfenv Exports: getInfoInFile, make.cdf.env, make.cdf.package, pmormm, read.cdffile ExportMethods: name.levels<-, name.levels, pbase.levels<-, pbase.levels, pbase<-, pbase, show, tbase.levels<-, tbase.levels, tbase<-, tbase ExportClasses: Cdf Package: marray Exports: controlCode, mapGeneInfo, widget.mapGeneInfo, htmlPage, opVersionID, table2html, rbind.marrayInfo, cbind.marrayRaw, cbind.marrayNorm, maNum2Logic, maGeneTable, maCompPlate, maInd2Coord, maCoord2Ind, maCompCoord, maCompInd, maCompLayout, maGenControls, maDotsMatch, maPlate<-, maControls<-, read.marrayLayout, read.marrayInfo, read.marrayRaw, read.Spot, read.GenePix, read.Agilent, read.Galfile, read.SMD, checkTargetInfo, maNormMain, maNorm, maNormScale, maMed, maNormMed, maLoess, maNormLoess, ma2D, maNorm2D, maMAD, maNormMAD, maCompNormEq, maCompNormA, write.marray, write.xls, write.list, plot.marrayRaw, plot.marrayNorm, maDotsDefaults, maDefaultPar, maBoxplot, maPlot.func, maText, maLowessLines, maLoessLines, maLegendLines, maPlot, maImage.func, maImage, maPalette, maColorBar, maTop, maSelectGnames, stat.confband.text, stat.gnames, findID, mean.na, var.na, cor.na, length.na, log.na, quantile.na, order.na, scale.na, prod.na, rm.na, widget.marrayLayout, widget.marrayInfo, widget.marrayRaw, widget.TwoSamples, maTwoSamples, sum.na, URLstring, maInfo, addLines, addText, addPoints, URLstring, read.fname ExportMethods: maLabels, maLabels<-, maInfo<-, maInfo, maNgc<-, maNsr<-, maNsc<-, maNspots<-, maPlate<-, maControls<-, maLayout<-, maGnames<-, maTargets<-, maW<-, maGf<-, maRf<-, maGb<-, maGb<-, maRb<-, maRb<-, maA<-, maM<-, maMloc<-, maMscale<-, maNotes<-, coerce, maNspots, maNgr<-, maNgc, maNsr, maNsc, maSub, maPlate, maNotes, maGridRow, maGridCol, maSpotRow, maSpotCol, maPrintTip, maRf, maGf, maRb, maGb, maW, maLR, maLG, maM, maA, maLayout, maNgr, maSpotCol, maControls, maNsamples, maGnames, maTargets, maA, maMloc, maMscale, maControls, maNormCall, boxplot, image, points, text, lines, summary, maNotes, show, [ ExportClasses: marrayInfo, marrayLayout, marrayRaw, marrayNorm, ShowLargeObject Package: mdqc Exports: mdqc, prcomp.robust Package: multtest Exports: MTP, as.list, mt.maxT, mt.minP, mt.plot, mt.rawp2adjp, mt.reject, mt.sample.label, mt.sample.rawp, mt.sample.teststat, mt.teststat, mt.teststat.num.denum, meanX, diffmeanX, FX, blockFX, twowayFX, lmX, lmY, coxY, get.Tn, boot.null, boot.resample, center.scale, fwer2gfwer, fwer2tppfp, fwer2fdr, get.index, ss.maxT, ss.minP, sd.maxT, sd.minP, wapply ExportMethods: as.list, plot, summary, update, [ ExportClasses: MTP Package: occugene Exports: checkFormat, delta0, eMult, etDelta, fCumul, fFit, occup2Negenes, unbiasB0, unbiasDelta0, varMult Package: oligo Exports: basecontent, cleanPlatformName, read.celfiles, read.xysfiles, sequenceDesignMatrix, list.celfiles, list.xysfiles, getPD, readSummaries, getCrlmmSummaries, crlmm, snprma, justSNPRMA, justCRLMM ExportMethods: $, antisenseThetaA, antisenseThetaB, boxplot, db, exprs, featureIndex, featureInfo, featureNames, geneNames, genomeBuild, geometry, getA, getM, getPlatformDesign, hist, image, initialize, kind, length, listFeatureFields, listFeatureSetFields, manufacturer, manufacturer<-, MAplot, mm, mm<-, mmindex, mmSequence, names, ncol, nProbes, nrow, platform, platform<-, platformDesignName, pm, pm<-, pmAllele, pmChr, pmindex, pmPosition, pmSequence, pmStrand, probeNames, rma, senseThetaA, senseThetaB, show Package: oligoClasses Exports: affyPlatforms ExportMethods: calculateCopyNumber, calls, calls<-, callsConfidence, callsConfidence<-, chromosome, chromosome<-, coerce, combine, copyNumber, copyNumber<-, cnConfidence, cnConfidence<-, db, initialize, position ExportClasses: SnpQSet, SnpCnvQSet, SnpLevelSet, SnpCallSet, SnpCopyNumberSet, oligoSnpSet, SnpCallSetPlus, SnpCnvCallSetPlus, FeatureSet, QuantificationSet, ExpressionFeatureSet, SnpFeatureSet, SnpCnvFeatureSet, TilingFeatureSet, ExonFeatureSet, GeneFeatureSet, PDInfo, DBPDInfo, SNPPDInfo, SNPCNVPDInfo, AffyTilingPDInfo, AffyExpressionPDInfo, AffySNPPDInfo, AffySNPCNVPDInfo, AffyGenePDInfo, ExpressionPDInfo, NgsExpressionPDInfo, TilingPDInfo, NgsTilingPDInfo, platformDesign Package: pamr Exports: pamr.adaptthresh, pamr.batchadjust, pamr.confusion, pamr.cv, pamr.fdr, pamr.from.excel, pamr.decorrelate, pamr.geneplot, pamr.knnimpute, pamr.knnimpute.old, pamr.listgenes, pamr.makeclasses, pamr.menu, pamr.cube.root, pamr.indeterminate, pamr.pairscore, pamr.plotcen, pamr.plotcvprob, pamr.plotcv, pamr.plotfdr, pamr.predictmany, pamr.predict, pamr.score.to.class1, pamr.score.to.class2, pamr.surv.to.class2, pamr.confusion.survival, pamr.plotsurvival, pamr.plotstrata, pamr.pvalue.survival, pamr.to.excel, pamr.train, print.pamrtrained, print.pamrcved, pamr.test.errors.surv.compute, pamr.xl.compute.offset, pamr.xl.error.trace, pamr.xl.get.offset, pamr.xl.derive.adjusted.prior, pamr.xl.get.default.training.parameters, pamr.xl.get.uniform.prior, pamr.xl.get.sample.prior, pamr.xl.get.class.names, pamr.xl.get.class.labels, pamr.xl.get.number.of.classes, pamr.xl.process.data, pamr.xl.compute.cv.confusion, pamr.xl.compute.confusion, pamr.xl.is.a.subset, pamr.xl.listgenes.compute, pamr.xl.plot.test.probs.compute, pamr.xl.plot.training.error.compute, pamr.xl.plotcen.compute, pamr.xl.plotcv.compute, pamr.xl.plotcvprob.compute, pamr.xl.predict.test.class, pamr.xl.predict.test.class.only, pamr.xl.predict.test.probs, pamr.xl.test.data.impute, pamr.xl.test.errors.surv.compute, pamr.xl.test.errors.compute, pamr.xl.transform.class.labels, pamr.xl.transform.data, pamr.xl.transform.test.data, pamr.xl.plotsurvival, pamr.xl.plotsurvival.test, pamr.xl.predict.test.surv.class, pamr.xl.plotsurvival.strata, pamr.xl.test.get.soft.classes, pamr.xl.get.threshold.range, pamr.xl.get.soft.class.labels Package: pathRender Exports: rendercMAPPathway, graphcMAP, pwayRendAttrs, reduceES, plotExGraph, colorNodes ExportMethods: plot ExportClasses: pwayGraph, coloredGraph Package: pcaMethods Exports: pca, nni, plotPcs, ppca, bpca, nipalsPca, svdPca, prep, Q2, svdImpute, checkData, kEstimate, llsImpute, nlpca, plotR2, fitted.pcaRes, kEstimateFast, asExprSet, robustSvd, robustPca ExportMethods: slplot, summary, print, fitted ExportClasses: pcaRes, nniRes, nlpcaNet Package: pdInfoBuilder ExportMethods: chipName, makePdInfoPackage, initialize ExportClasses: PkgSeed, PDInfoPkgSeed, AffyExpressionPDInfoPkgSeed, AffyTilingPDInfoPkgSeed, AffySNPPDInfoPkgSeed, AffySNPCNVPDInfoPkgSeed, AffyGenePDInfoPkgSeed, NgsPDInfoPkgSeed, NgsExpressionPDInfoPkgSeed, NgsTilingPDInfoPkgSeed Package: pdmclass Exports: pdmClass, pdmGenes, pdmClass.cv, predict.pls, predict.svd Package: pkgDepTools Exports: getInstallOrder, makeDepGraph Package: plw Exports: estimateMVbeta, estimateSigmaMVbeta, estimateSigmaMV, estimateSigma, getKnots, lmw, plw, scaleParameterPlot, topRankSummary, varHistPlot, plotSummaryLog2FC, plotSummaryT, logitTTransform, logitTStat, studenttTTest, madByIndex, meanByIndex, medianByIndex, orderStatByIndex, sdByIndex, meanSdByRow, HowToPLW Package: ppiStats Exports: assessSymmetry, bpMatrix, calcInOutDegStats, degreeEstimates, estErrProbMethodOfMoments, estimateCCMErrorRates, genBPGraph, idHomodimers, idStochastic, idSystematic, idViableProteins, nullDistDoublyTestedEdges, ppiBuildParams4GO, ppiHGTest4GO, ppiBuildParams4PFAM, ppiHGTest4PFAM, twowayPERM, findDegree, makeBinVect, estimatePPIErrorRates, createSummaryTables, viabilityCharts, inOutScatterCharts, separateExptBySize Package: prada Exports: analysePlate, as.all, barploterrbar, combineFrames, csApply, fitNorm2, getPradaPar, plotNorm2, devDims, plotPlate, readCytoSet, readFCS, read.fcs, removeCensored, setPradaPars, thresholds, threePanelPlot, devRes, .drawCircle, .drawPie, vpLocation, touchFCS, combineGates, progress, updateProgress, killProgress ExportMethods: colnames, colnames<-, description, description<-, exprs, exprs<-, length, [, [[, [[<-, pData, phenoData, phenoData<-, show, plot, gate, applyGate, drawGate, gate<-, names, names<-, as.gateSet, nrow, ncol, appendGates, lines, split ExportClasses: cytoFrame, cytoSet, gate, gateSet Package: quantsmooth Exports: quantsmooth, quantsmooth.seg, quantsmooth.cv, getLambdaMin, plotSmoothed, getChangedRegions, getChangedIdx, numericCHR, characterCHR, scaleto, plotChromosome, prepareGenomePlot, paintCytobands, lengthChromosome, drawSimpleChrom, position2Cytoband, grid.chromosome Package: rama Exports: arrange.row, est.shift, fit.model, is.row.na, ls.effect, mat.mean, ratio.plot, weight.plot Package: rbsurv Exports: rbsurv Package: rflowcyt Exports: ContourScatterPlot, standard, boxplot.FCS, plotdensity.FCS, plotECDF.FCS, plotvar.FCS, parallelCoordinates, ImageParCoord, read.FCS, read.series.FCS, convertS3toS4, make.grid, make.density, pairs.CSP, legend.CSP, metaData, percentile.FCS, PercentPos.FCS, ProbBin.FCS, breakpoints.ProbBin, createGate, emp.f, extractGateHistory, extractGatedData, fcs.type.facscan256, get.h, get.num.modes, get.p, pkci2.flowcytest, summary.ProbBin.FCS, runflowcytests, plot2sets.FCS, plotQA.FCS, MODE, icreateGate, showgate.FCS, JointImageParCoord, plot.ProbBin.FCS, KS.flowcytest, WLR.flowcytest, ROC.FCS, rect.box.idx ExportMethods: print, show, summary, plot, fluors, addParameter, checkvars, coerce, dim.FCS, equals, fixvars ExportClasses: FCS, FCSmetadata, FCSsummary, FCSgate Package: rtracklayer Exports: genomeBrowsers ExportMethods: activeView, activeView<-, browseGenome, browserSession, browserView, browserViews, chrid, close, dataVals, export, export.bed, export.gff, export.gff1, export.gff2, export.gff3, export.ucsc, export.wig, genomeSegment, genomeSegment<-, genomeSequence, import, import.bed, import.gff, import.gff1, import.gff2, import.gff3, import.ucsc, import.wig, laySequence, layTrack, merge, featChrom, featStart, featEnd, featStrand, trackData, trackSet, trackSets, tracks, tracks<-, ucscTable, ucscTrackModes, ucscTrackModes<-, coerce, initialize, show, [ ExportClasses: genomeSegment, chrid, trackSet, trackSets, browserSession, browserView, ucscSession, ucscView, argoSession, argoView, ucscTrackSet, ucscTrackLine, basicTrackLine, wigTrackLine, ucscTrackModes Package: seqLogo Exports: seqLogo, makePWM ExportMethods: plot, summary, print, show ExportClasses: pwm Package: siggenes Exports: args.ebam, args.finda0, args.sam, ebam, ebam2excel, ebam2html, filterALL, find.a0, fudge2, help.ebam, help.finda0, help.sam, link.genes, link.siggenes, list.siggenes, pi0.est, plotArguments, sam, sam2excel, sam2html, sam.plot2, sam.dstat, sam.wilc, sam.snp, d.stat, cat.stat, wilc.stat, z.ebam, cat.ebam, wilc.ebam, z.find, denspr, rowWilcoxon, rowRanksWilc, na.handling, nclass.wand, findDelta, qvalue.cal, chisqClass ExportMethods: show, print, plot, summary, identify ExportClasses: SAM, EBAM, FindA0, sumSAM, sumEBAM Package: simpleaffy ExportMethods: [, avbg, calculated.from, calls, fc, get.array.subset, group, maxbg, means, members, minbg, pData, percent.present, plot, qc, qcProbes, ratios, sfs, spikeInProbes, target, tt ExportClasses: PairComp, QCStats Package: sizepower Exports: sampleSize.randomized, sampleSize.matched, power.randomized, power.matched, power.multi Package: snpMatrix Exports: epsout.ld.snp, glm.test.control, ibs.stats, ibsCount, ibsDist, ld.snp, ld.with, niceprint, pair.result.ld.snp, plot.snp.dprime, print.snp.dprime, qq.chisq, read.HapMap.data, read.pedfile.info, read.snps.chiamo, read.snps.long, read.snps.long.old, read.snps.pedfile, read.wtccc.signals, row.summary, single.snp.tests, snp.cbind, snp.rbind, snp.cor, snp.lhs.tests, snp.post, snp.pre, snp.rhs.tests, write.snp.matrix, xxt ExportMethods: cbind2, is.na, ld.with, rbind2, show, summary, [, [<-, coerce, initialize ExportClasses: snp.matrix, X.snp.matrix, snp, X.snp, snp.dprime Package: splots Exports: plotScreen Package: stam Exports: stam.net, stam.cv, stam.fit, stam.predict, stam.evaluate, stam.writeHTML, stam.graph.plot, stam.rgb.colors, stam.serve ExportMethods: getGOterm, getGOchildren, getGOparents, writeHTML, print, initialize ExportClasses: stamNode, stamINode, stamLeaf, stamNet, stamFit, stamCV, stamPrediction, stamEval Package: tilingArray Exports: normalizeByReference, segment, costMatrix, findSegments, sampleStep, readCel2eSet, posMin, otherStrand, plotAlongChrom, plotAlongChromLegend, plotSegmentationHeatmap, plotSegmentationDots, plotFeatures, comparisonPlot, plotPenLL, qcPlots, PMindex, BGindex, segChrom, residuals.breakpointsPretend, breakpoints.breakpointsPretend ExportMethods: plot, show, confint, logLik ExportClasses: segmentation Package: tkWidgets Exports: DPExplorer, args2XML, argsWidget, dataViewer, dbArgsWidget, eExplorer, fileBrowser, fileWizard, find.type, guess.header, guess.sep, importPhenoData, importWizard, listSelect, objViewer, objectBrowser, pExplorer, pickItems, tkMIAME, tkSampleNames, tkphenoData, vExplorer, viewVignette, WLValue<-, WName, WRButtons, values.Widget, WValue, WValue<-, WbuttonFun, WbuttonText, WcanEdit, WfromText, WpostFun, WpreFun, WtoText, WwList, WwList<-, print.Widget, WLValue, WEnd, appendSepDir, getWvalues, hasChar, stdType, objNameToList, getPkgContents, getFileContents, pickFiles, pickObjs, print.pWidget, hasPrefix, hasSuffix, hasChar, formatArg ExportClasses: colInfo Package: topGO Exports: annFUN.db, annFUN, annFUN.gene2GO, annFUN.GO2genes, GOplot, showSigOfNodes, getPvalues, groupGOTerms, reverseArch, getGraphRoot, buildGOgraph.topology, inducedGraph, buildLevels, getNoOfLevels, mapGenes2GOgraph, .sigAllMethods, .getFromNode, .genesInNode, .countsInNode, .writeToNodes ExportMethods: initialize, description, ontology, allGenes, feasible, graph, geneSelectionFun, description<-, ontology<-, feasible<-, graph<-, geneSelectionFun<-, print, show, updateGenes, genes, numGenes, geneScore, sigGenes, numSigGenes, usedGO, attrInTerm, genesInTerm, scoresInTerm, countGenesInTerm, termStat, updateTerm<-, allMembers, Name, members, testStatistic, Name<-, allMembers<-, members<-, numMembers, numAllMembers, runTest, sigMembers<-, sigAllMembers, numSigAll, sigMembers, numSigMembers, contTable, allScore, membersScore, score<-, rankMembers, pType, pType<-, membersExpr, getSigGroups, elim, cutOff, elim<-, cutOff<-, updateGroup, Weights<-, Weights, sigRatio<-, getSigRatio, score, testName, testClass, score<-, testName<-, testClass<-, printGenes, penalise, scoreOrder, testStatPar, printGraph, GenTable, GOFisherTest, GOKSTest, GOtTest, GOglobalTest, joinFun, allParents, expressionMatrix, phenotype ExportClasses: topGOdata, topGOresult, groupStats, classicCount, classicScore, classicExpr, removeCount, removeScore, removeExpr, elimCount, elimScore, elimExpr, weightCount, pC, parentChild Package: vbmp Exports: vbmp, predictCPP, predError, predLik, predClass, covParams, plotDiagnostics Package: vsn Exports: vsn, vsnh, vsnPlotPar, getIntensityMatrix, normalize.AffyBatch.vsn, vsnMatrix, justvsn, vsnrma, sagmbAssess, sagmbSimulateData, plotVsnLogLik, scalingFactorTransformation ExportMethods: vsn2, meanSdPlot, predict, logLik, coef, coefficients, show, exprs, nrow, ncol, dim, coerce ExportClasses: vsn, vsnInput Package: widgetInvoke Exports: createWF, widgetInvoke, fun2wFun, writeWIxml, readWIxml, testWIfun ExportMethods: argDefault, argLocation, argName, argRequired, argType, argWidgetType, funName, funArgList, nItems, itemNames, defaultValue, returnType ExportClasses: wFun, funArg, SimpleW Package: widgetTools Exports: button, checkButton, dropdownList, entryBox, env<-, funs, funs<-, label, listBox, makeViewer, oneVScrList, pWidgets, getListOption, pWidgets<-, postFun, postFuns<-, preFun, preFuns<-, radioButton, textBox, tooltip, widget, writeList, writeText, vName, vName<-, wEnv, wEnv<-, wFuns, wFuns<-, wHeight, wHeight<-, wName, wName<-, wNotify, wNotify<-, wPostFun, wPostFun<-, wPreFun, wPreFun<-, wTitle, wTitle<-, wType, wType<-, wValue, wValue<-, wView, wView<-, safeFileOpen, widgetView, getListValue, getTextValue, getEntryValue ExportClasses: basicPW, widget, widgetView Package: xcms Exports: etg, medianFilter, retexp, specNoise, specPeaks, SSgauss, xcmsRaw, xcmsSet ExportMethods: cdfpaths, cdfpaths<-, diffreport, fillPeaks, findPeaks.centWave, findPeaks.matchedFilter, findPeaks.MSW, findPeaks, getEIC, getPeaks, getScan, getSpec, group, groupidx, groupidx<-, groupnames, groups, groups<-, groupval, mzrange, peaks, peaks<-, plotChrom, plotPeaks, plotRaw, plotrt, plotScan, plotSpec, plotSurf, plotTIC, profinfo, profinfo<-, profMedFilt, profMethod, profMethod<-, profMz, profRange, profStep, profStep<-, rawEIC, retcor, revMz, rtrange, sampclass, sampclass<-, sampnames, sampnames<-, show, sortMz ExportClasses: xcmsEIC, xcmsRaw, xcmsSet Package: xps Exports: import.expr.scheme, import.exon.scheme, import.genome.scheme, import.data, export.scheme, export.data, export.expr, export.call, export.filter, export.root, rma, mas4, mas5, mas5.call, dabg.call, bgcorrect, normalize, summarize, express, bgcorrect.mas4, bgcorrect.mas5, bgcorrect.rma, bgcorrect.gc, normalize.constant, normalize.quantiles, normalize.lowess, normalize.supsmu, summarize.mas4, summarize.mas5, summarize.rma, boxplot.dev, image.dev, mvaplot.dev, prefilter, unifilter, ProjectInfo, PreFilter, UniFilter, root.scheme, root.data, root.image, root.graph1D, root.graph2D, root.mvaplot, root.hist1D, root.hist2D, root.hist3D, root.density, xpsOptions, debug.xps, getDatatype, validTreetype, getChipName, getChipType, getNameType, getProbeInfo, getNumberTrees, getTreeNames, isROOTFile, existsROOTFile, type2Exten ExportMethods: filterTreeset, validFilter, volcanoplot, callTreeset, exprTreeset, fcFilter, fcFilter<-, unitestFilter, unitestFilter<-, uniTest, uniTest<-, callFilter, callFilter<-, cvFilter, cvFilter<-, diffFilter, diffFilter<-, gapFilter, gapFilter<-, highFilter, highFilter<-, lowFilter, lowFilter<-, madFilter, madFilter<-, quantileFilter, quantileFilter<-, ratioFilter, ratioFilter<-, varFilter, varFilter<-, numberFilters, pvalData, pvalData<-, presCall, presCall<-, validCall, callplot, exprs, exprs<-, exprType, exprType<-, mvaplot, normType, normType<-, se.exprs, xpsPreFilter, xpsUniFilter, addData, attachBgrd, attachInten, background, background<-, bgtreeNames, image, intensity, intensity<-, mm, pm, pmplot, rawCELName, removeBgrd, removeInten, validBgrd, xpsBgCorrect, xpsDABGCall, xpsMAS5Call, xpsMAS5, xpsMAS4, xpsNormalize, xpsPreprocess, xpsSummarize, xpsRMA, boxplot, getTreeData, hist, mboxplot, schemeFile, schemeFile<-, schemeSet, schemeSet<-, validData, attachMask, chipMask, chipMask<-, chipName, chipType, chipType<-, ncols, nrows, probeInfo, removeMask, export, fileDir, fileDir<-, initialize, root.browser, rootFile, rootFile<-, setName, setName<-, setType, setType<-, treeNames, arrayInfo, arrayInfo<-, authorInfo, authorInfo<-, biopsyInfo, biopsyInfo<-, cellineInfo, cellineInfo<-, datasetInfo, datasetInfo<-, hybridizInfo, hybridizInfo<-, primcellInfo, primcellInfo<-, projectInfo, projectInfo<-, sampleInfo, sampleInfo<-, show, sourceInfo, sourceInfo<-, tissueInfo, tissueInfo<-, treatmentInfo, treatmentInfo<- ExportClasses: ProjectInfo, TreeSet, Filter, PreFilter, UniFilter, SchemeTreeSet, ProcesSet, DataTreeSet, ExprTreeSet, CallTreeSet, FilterTreeSet, AnalysisTreeSet Package: yaqcaffy Exports: reprodPlot, getSpikeProbes, getBioProbes, getRatioProbes, getQCRatios, getAllInt, getOutliers, yaqc.plot ExportMethods: avns, bioCalls, gcosProbes, moreSpikeInProbes, isLog, arrays, plot, show, yaqc, merge ExportClasses: YAQCStats