47ed248104ddf80041498219a7afb505 *DESCRIPTION
73f9645a546038e1992a99cf59017b0c *NAMESPACE
9400b3c4ffcd01c344a61387d7131750 *R/000.R
646155cdee987c9e73189073bc88c53b *R/006.fixVarArgs.R
dc193ab3c1d3cf0b5cd9400752585fa5 *R/009.setup.R
94bf454cc3e6953b6feb80599602b47e *R/999.AromaAffymetrix.R
f8432ab6980dd3ca0c6f967082ce5958 *R/999.DEPRECATED.R
dcb0e44d79e9859ee6006eb8c70b2837 *R/999.NonDocumentedObjects.R
42e2ff0a085b6cef63c0678cb6b9c5df *R/999.package.R
6af401f75860403b7ef1bec61a5e49b5 *R/ASCRMAv2.R
a8b212ada010bafdcce8e45dfe4d1cd1 *R/AbstractProbeSequenceNormalization.R
ab859a8f905b5dcc9b02cd9ae0408352 *R/AdditiveCovariatesNormalization.R
af938f2ccd21e80f31b852a609ac9d66 *R/AffineCnPlm.R
7c836ad3b9192597c74dffbb0c9180ab *R/AffinePlm.R
7f486e6fb21cdf532bde10425cb32909 *R/AffineSnpPlm.R
4c0482fe72f77c24ac65a06ee64e19ea *R/AffyGenePDInfo.writeCdf.R
9d3b3364031b8a044ccf1fe07d3d1142 *R/AffymetrixAptSummaryFile.R
7f3154f0137a847ddc3a89f82a690157 *R/AffymetrixCdfFile.COUNTS.R
fc424f8c1b6297f20a1b4b110c497dbe *R/AffymetrixCdfFile.MONOCELL.R
dc999943de6ac6744321ac90c64221c1 *R/AffymetrixCdfFile.PLOT.R
fd630e9ce1ad32e2724d1946f382f2e4 *R/AffymetrixCdfFile.R
200656847d3e9dc14c656b8b9e22e28c *R/AffymetrixCdfFile.SNPs.R
00d169b1a0e400e11ef220c05afe58d9 *R/AffymetrixCdfFile.UNIQUE.R
63add48886fd5fffded7f43b7321834e *R/AffymetrixCdfFile.computeAffinities.R
66636011a9c99f29648921c27589f394 *R/AffymetrixCdfFile.getAlleleCellPairs.R
bd8378f44a9d5cb0dea118d1bd583141 *R/AffymetrixCdfFile.getAlleleProbePairs.R
65f2591f45e0f15c8f20a9506705dfb4 *R/AffymetrixCdfFile.getAlleleProbePairs2.R
f26ba54775c144a0b22dd73f597f5903 *R/AffymetrixCdfFile.getAlleleProbePairs3.R
5a97ea568afaddfa5d2a2e1dc8595a2c *R/AffymetrixCdfFile.getCellQuartets.R
bc92dacf16d7f61b511d50ebcadb2796 *R/AffymetrixCdfFile.getProbeSequenceData.R
58e54350df26dd2a0e600307832ae660 *R/AffymetrixCdfFile.getSubsetOfCellIndices.R
d4cf0ead48b8b18522ff46792bb4627e *R/AffymetrixCdfFile.getSubsetOfUnits.R
4dc465845510c5ff7e4907ab6a5b88de *R/AffymetrixCdfFile.getUnitGroupCellMap.R
f0a44546838e2409e94e638881699863 *R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R
940ad7f9d151b6dd46166546c2e6ebe3 *R/AffymetrixCdfFile.groupUnitsByDimension.R
b6358105e28866ab6b80ae3ea870387a *R/AffymetrixCdfFile.readDataFrame.R
60b8a7b1e946aab9ec84ee8e9416be2c *R/AffymetrixCdfFile.writeCdfByExcludingCells.R
0a3f4053242421028caa42b1913d1b7d *R/AffymetrixCelFile.BG.R
c1778f4fb5ceb6491cf300916fabdf9d *R/AffymetrixCelFile.PLOT.R
67a13fe5f53c54d54224e927d9d2a80d *R/AffymetrixCelFile.R
493a56b1077b67934f6f2858a4472bfa *R/AffymetrixCelFile.allocateFromCdf.R
ef79b7a95f6fb9431c856a67fbac88d7 *R/AffymetrixCelFile.createFrom.R
b2a18bcdece6dc81b42a906fd79e8190 *R/AffymetrixCelFile.extractMatrix.R
46d0e82ad944fa43f001da59191f1535 *R/AffymetrixCelFile.fitQuantileNormFcn.R
7b48de212e456e4c415d999fde18f641 *R/AffymetrixCelFile.normalizeAffine.R
5906674cfd5f93f4fc7b9895502c7ae3 *R/AffymetrixCelFile.normalizeQuantile.R
589aa832a4a3cb4d2031271c402397bd *R/AffymetrixCelSet.BG.R
659ef412c3f26a15e8f630f44b7d714e *R/AffymetrixCelSet.NORM.R
7a42b3bd212be3887d1bbecbade75ccd *R/AffymetrixCelSet.PLOT.R
07412e20ebe0edaa89492f0810b2e988 *R/AffymetrixCelSet.R
15a4eedf1f19af22c6977f1fb34d97dc *R/AffymetrixCelSet.convertToUnique.R
fb8a7812df7b0c95197fe8f8eac70538 *R/AffymetrixCelSet.extractAffyBatch.R
740f84f82fe43b70ce674490ef075e33 *R/AffymetrixCelSet.extractMatrix.R
4a3f890b66fbe3e9bdfc19fd6aa77ba6 *R/AffymetrixCelSet.extractSnpFeatureSet.R
805ff2fa1b8e5b4e843f96bb6ea62ece *R/AffymetrixCelSet.getAverageFile.R
c7d07a70cb44cee9114450d9f5b73912 *R/AffymetrixCelSet.importFromDChip.R
1c8dec2c9ad5de8dd01052968d8e1807 *R/AffymetrixCelSet.justSNPRMA.R
01ff15c649a90d8659318e2b011ec9c3 *R/AffymetrixCelSet.writeSgr.R
c5676be05dbc266ccf58083b87f62089 *R/AffymetrixCelSetReporter.R
062f51ec0c233a97bf35257184021569 *R/AffymetrixCelSetTuple.R
b422f13642cac7faa4c11600d44c3d53 *R/AffymetrixCnChpFile.R
1087b594a5ed6ec694225e772ed65444 *R/AffymetrixCnChpSet.R
dc3daab0d19ef92b3a68b621ba4186cd *R/AffymetrixCnChpSet.extras.R
3fe354899512e3c75cebc189e58e393e *R/AffymetrixCsvFile.R
98b9a37404088ea4a52fa40f1cf8c157 *R/AffymetrixCsvGenomeInformation.R
5dabb3205e258296f7a12cd4a56ee9e7 *R/AffymetrixFile.R
39b1912c3aefbc3a68745581e8bf8a5a *R/AffymetrixFileSet.R
dc23c4313d3428faa576597ff0ec7d90 *R/AffymetrixFileSet.getIdentifier.R
0ad98804c68ab7a42314ec725d039a13 *R/AffymetrixFileSetReporter.R
9d852364b24adede27784bac1b998ffc *R/AffymetrixNetAffxCsvFile.R
05d3fd51717d57099b7727e6e182ca62 *R/AffymetrixNetAffxCsvFile.XTRS.R
5b21fa7dfbf295a1981b7f3a69ffbcef *R/AffymetrixPgfFile.R
8b384a51cc546ccc336bd532c1a631db *R/AffymetrixPlatform.R
11df071b0debda233d93ef2bcb3f37ae *R/AffymetrixProbeTabFile.R
61b68a29f70729251038be096a70c273 *R/AffymetrixTabularFile.R
c11a6c8d20f87aef99e31adf2e5f7943 *R/AffymetrixTsvFile.R
ef339c687d3ee7a3811d02b534a223fc *R/AlleleSummation.R
e1b52cc0298380d1a8f4a175cbfe7c4e *R/AllelicCrosstalkCalibration.PLOT.R
8a24dd8ea57b8a98aa9cf09fb98566a0 *R/AllelicCrosstalkCalibration.R
1c91dccd5013bf3d659b82c9392d8485 *R/AllelicCrosstalkCalibration.getSetsOfProbes.R
de1bb850b37d0f2d0c578336222a49d0 *R/AromaCellCpgFile.AFFX.R
9c4a4794511dea54104b5cbb2ce11847 *R/AromaCellMatchScoreFile.AFFX.R
5d05fb7aa508bb85d8ecf4889a2505a3 *R/AromaCellMatchScoreFile.R
187655af33764b1c7b306883aa8200c1 *R/AromaCellMatchScoreFile.importFromBpmap.R
bcd44b82ac924324df0666505a82e6ef *R/AromaCellPositionFile.AFFX.R
6cb9dd9b712f7a04dad09be94f7d2d64 *R/AromaCellSequenceFile.AFFX.R
bc017d8dd61c1539e27553f2999bf515 *R/AromaCellSequenceFile.importFromBpmap.R
d0a410ae12d1c454106372cdf13e33a3 *R/AromaChipTypeAnnotationFile.R
9918a6428d0d65e5bc8728f8bcc16638 *R/AromaPipeline.R
45ad84b7f60e7cd4eb677f5418aad2a6 *R/AromaUfcFile.R
5528142cca73f7e6bcde221969ebe88c *R/AromaUflFile.AFFX.R
3afeae1ad1c21f3be2829fda191a653d *R/AromaUgpFile.AFFX.R
1d7fcaf120f60d752e7fc85675629166 *R/AromaUnitGcContentFile.AFFX.R
4b6bef7bfdc8e508d67a006ca2ba027f *R/AromaUnitTabularBinaryFile.AFFX.PLOT.R
92ee7e1b10cbeb06ba273dd918d56ba5 *R/AromaUnitTabularBinaryFile.AFFX.R
84290b07b85b92868ba9beb40dcfe407 *R/ArrayExplorer.R
7f54fae5a8b96fdb877253492e94fcd2 *R/AvgCnPlm.R
0ab22c2ac1061d0e14802c233c89ae0c *R/AvgPlm.R
638f2ed470c7fb348bcf165e266e5452 *R/AvgSnpPlm.R
279ac36b9d100c2d7470b62826a8befb *R/BackgroundCorrection.R
0c89174389902e5a64c284aebf3e38a0 *R/BaseCountNormalization.R
2074c55f46519bd7dcb764bfd6e3c8a6 *R/BasePositionNormalization.R
dd8898688cee0d01b8ec41a267290476 *R/BasePositionNormalization.getFit.R
cd866b916c18604d262f90813e453b64 *R/ChipEffectFile.R
d16b4dbe009d5eb614b74d31e5b9493b *R/ChipEffectFile.TOFULL.R
8354315fd5473f89b90013897f343501 *R/ChipEffectFile.extractTheta.R
52a59f857ff71b03f68ce0590cdf0ca1 *R/ChipEffectFile.fromDataFile.R
c865b3c51fb37d787a6b5b43f67a980b *R/ChipEffectFile.getUnitGroupCellMatrixMap.R
c9456d8d16ae0438da60b4093b6666f0 *R/ChipEffectFile.xam.R
8a1d722339bc5ae9258d1023acf501bf *R/ChipEffectGroupMerge.R
5be336f9817c0de390e07a0a19a5502b *R/ChipEffectNnn.extractChromosomalDataFrame.R
9315e41742e13ec8afcf5e13bdf1d18d *R/ChipEffectSet.PLOT.R
672e80c6885bc743f91c52b89728d8f0 *R/ChipEffectSet.R
2453b7aba45dbb65f6840cb2f15dbc42 *R/ChipEffectSet.STATS.R
223696f2a3644ec3aa0469e745a28612 *R/ChipEffectSet.TOFULL.R
9bdc283edd1661ca6085d5ef28a36f38 *R/ChipEffectSet.calculateBaseline.R
18bf89c6f08ca1879b9a80f3e037775d *R/ChipEffectSet.extractExpressionSet.R
61ac5af168ea27f2e71c51c38f30e70c *R/ChipEffectSet.extractTheta.R
8cced7d1d317ecd7283d0f9b742f1db6 *R/ChipEffectSet.getBaseline.R
96f4eaee531c3f095dbf0f31fc08f723 *R/ChipEffectSet.xam.R
45c95eb30f815da0add6f5c25bfe1f2d *R/ChipEffectSetTuple.R
575735cb5246bd5da24a48995c39abd6 *R/ChipEffectTransform.R
058de468d5c96289ba0040a837b5469e *R/ChromosomalModel.AFFX.R
a282fdfc67dcaf153523fac0e911a400 *R/ChromosomalModel.getPositionChipTypeUnit.R
4fed875c451c1394ee96f57bcaf4bc59 *R/ChromosomalModel.getXTheta.R
0467a87277e6da6b200771dfff35a579 *R/CnChipEffectFile.R
b871fa6332428e3c8bf5a126ebe0e06a *R/CnChipEffectFile.exportAromaSignalBinaryFileList.R
7691eab622abccdfc639735765c2be84 *R/CnChipEffectSet.R
143811258101887c78dac096506ff4b9 *R/CnChipEffectSet.importFromApt.R
c82b01cca1d1c38ab2f58b788e17c01a *R/CnChipEffectSet.importFromDChip.R
dd1f3aa432496c87fadc6cc374e0ae4f *R/CnChipEffectSet.writeWig.R
885557e308583eab6b5790f8bfe215a7 *R/CnChipEffectSetTuple.R
f32b39503be50c0abe13b58d43ef8e51 *R/CnPlm.R
2e93a6a9d80465f931d11face5a04858 *R/CnProbeAffinityFile.R
791b5d701adfd50b1a104d6504e809c2 *R/CnagCfhFile.R
6f0984a6e3a92c4ad326fec778f91a3a *R/CnagCfhSet.R
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f4abcae38c717d35434d49b3b9b154ed *R/CopyNumberSegmentationModel.migrateTool.R
1231d59e7d8402287c541943eb10b3b7 *R/CrlmmModel.EXT.R
b16e385713841c8385f5e7b7212d9d38 *R/CrlmmModel.R
ceb9482694760429bd70a6eaa3d55ebd *R/CrlmmParametersFile.R
7d1f55fb2e3ba27bffd9639117af5a4f *R/CrlmmParametersSet.R
9982949ee49c2182813477c8a8d2a185 *R/DChipCdfBinFile.R
a2bd9332769c3d60914e966bf2142f3b *R/DChipCdfBinFile.mapToUnitNamesFile.R
df1ce5a737320ee20be25f06d2fe07be *R/DChipDcpFile.R
d65e7c3cc6cefa9708f2ba058a30f752 *R/DChipDcpSet.R
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dd46b6045735bc6a68b4cfb9b089002c *R/DChipGenomeInformation.R
e856ca25a2e923608ef8dff0c9207c0d *R/DChipQuantileNormalization.R
d24b177d0b1fe5cb9f1ce430d0b91617 *R/DChipSnpInformation.R
93da0a141ea791ed2a4e8842defe11a0 *R/ExonChipEffectFile.R
a84344430f6c16e3b6334b9a8d1b1f74 *R/ExonChipEffectSet.R
ab185d1e55857c6c7a8bfc81760fadb6 *R/ExonProbeAffinityFile.R
06a35cb31331131d1bea505d04661ebd *R/ExonRmaPlm.R
2fea25086c96da6e4d74f7684b95cbb7 *R/ExonRmaPlm.calculateWeights.R
757c8d6483408abc38c966bd7748ed6e *R/FirmaFile.R
ed9c76241967a095e81ca46d375f0f00 *R/FirmaModel.R
889b5f1cc2da3caa0572a3ec7cfba999 *R/FirmaSet.R
b71ecbab7f1a9c0ee77943851cbd0223 *R/FragmentEquivalentClassNormalization.R
565acbceb3ad1ae2dc2d7b84572a26ad *R/FragmentLengthNormalization.R
86367ec48cee2fb37e04f6f860d8c5de *R/GcContentNormalization.R
87de9d5d2bc73be29cb498d44f7fc8e3 *R/GcContentNormalization2.R
7eebcd1ca32deb5ec0cadce5abc97e49 *R/GcContentNormalization2.plotCovariateEffects.R
75fa08e8cc4ca2e0bf996d342cbae560 *R/GcRmaBackgroundCorrection.R
13feec0316ead8316ddcfe55c4aedbb4 *R/GenericReporter.R
90d52a5eaee86651e805249e300bf83c *R/GenomeInformation.AFFX.R
07d1208fa74693750046f645f815dbd6 *R/GenomeInformation.R
20e2824e6d3c3f32b88ebb2bbd598a28 *R/HetLogAddCnPlm.R
03aa3ea0a0356d1e649d8f9c49497fdc *R/HetLogAddPlm.R
fbb44e1c2286833942d4b48e7e2a63ea *R/HetLogAddSnpPlm.R
5b70de85c7a301fd6ca55ba9691fd9ca *R/LimmaBackgroundCorrection.R
10e115082503474746987873ea836122 *R/LinearModelProbeSequenceNormalization.R
0a4415dd8f9b28638eec4d2f91d871fe *R/MatNormalization.R
bfa5c6c2b3834a5b20e7eeda8744230c *R/MatSmoothing.R
4386b68b4f5402ec9d364152efb3becd *R/MbeiCnPlm.R
126c444348cee9455979b4c594de9f68 *R/MbeiPlm.R
a4c8dd1598130ec4ee9c0161350fb7a2 *R/MbeiSnpPlm.R
c490f461736866472882b8befe4a4d01 *R/Model.R
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37ba624e4e9b7b58f20301a50eefc1c0 *R/NormExpBackgroundCorrection.R
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9388086af14d2145806a908149b6fa41 *R/Package.XTRA.R
6c469e75c660fdb835028fb8cdcbffe1 *R/ParameterCelFile.R
09c8392e04efef1142d31f84cc8b98a2 *R/ParameterCelFile.extractNnn.R
47755aa3b1170f315c5d812412a6211c *R/ParameterCelSet.R
9d57f99f5f1f5bdf5b1e63047324732c *R/ProbeAffinityFile.R
679a5735d99309c0d191cb2308ea0a6c *R/ProbeLevelModel.R
74066f6a76a351f12047cbd432af8ef5 *R/ProbeLevelModel.calculateResiduals.R
7db1e722c338bd5f4ea168d947809976 *R/ProbeLevelModel.calculateWeights.R
18a41854f2d07bfd7546d1d2ed1fd3b0 *R/ProbeLevelModel.fit.R
24c93673f00437946c68c8ee93141fc8 *R/ProbeLevelTransform.R
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36160aae6d25aa158a26d8b940dbea94 *R/QualityAssessmentFile.R
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7baab78faa6301d7a98ead4beb3d2a40 *R/QuantileNormalization.R
0b46865a2c68399caf944c9f45a6bfe7 *R/QuantileNormalization.xtra.R
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0d435a81e90221d5913a6271f9e9e973 *R/ResidualFile.R
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aed30e75863bcf487d146b1aa3acc660 *R/RmaBackgroundCorrection.R
2ad88cc209882d805dc2509d7efff011 *R/RmaCnPlm.R
66e6bec8947db3c724516a5679673aab *R/RmaPlm.R
025d49973a69311ebfc8d2871df78bd4 *R/RmaSnpPlm.R
d1956c62f37ba3e57f4575ab8495de32 *R/ScaleNormalization.R
86bced0050a009eedff2b3f0ac8e8ece *R/ScaleNormalization3.R
e102ca5dda9b45af1dd6673c4508a62b *R/SingleArrayUnitModel.R
1eb3c499cb87f07882de42a09877921c *R/SingleArrayUnitModel.fit.R
3477435df7d5b5601f3f2eef30f382b2 *R/SmoothMultiarrayModel.R
3f8fb8fe24287227ee40d0c511c15fd5 *R/SmoothMultiarrayModel.fit.R
d80c5c2e9704869e826dd0bc1c5ccb08 *R/SmoothRmaModel.R
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314602421853ba79caad94009f66cdee *R/SnpChipEffectFile.extractTotalAndFracB.R
8440767670472998918db3f133159be3 *R/SnpChipEffectGroupMerge.R
6b4cd8edc6f73ea5410d7950fd2b1c7a *R/SnpChipEffectNnn.extractCNT.R
3c33c0b92a71034bf1b680b3dbdf1c92 *R/SnpChipEffectNnn.writeCNT.R
16ac5fcfc8bcc1405c8e3ec8d46225c5 *R/SnpChipEffectSet.R
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045d0c2f2ed1e32b60fff6ee93f5903c *R/SnpChipEffectSet.extractAlleleSet.R
2e42be2d95c4924e00a93464dc6c6dc6 *R/SnpChipEffectSet.extractSnpCnvQSet.R
28fbc6e784aeff384f3192e67f7b1007 *R/SnpChipEffectSet.extractSnpQSet.R
d45c93541d8d79a05e0525ecbd369394 *R/SnpChipEffectSet.extractTotalAndFreqB.R
e41da8d1cac0535636736be4821751b6 *R/SnpCnvQSet.extractTheta.R
45045da2ca7c94454215acb44e2c8102 *R/SnpInformation.R
497d4a7c94d284c030f8591018978253 *R/SnpPlm.R
6b1c8e92fb7be791cbbc2f64ec388b1e *R/SnpProbeAffinityFile.R
bf5f30204865b2ddd14564a9efb4ed49 *R/SnpQSet.extractTheta.R
3f9048a2d87c01c7fdae6d01b94e2f6c *R/SpatialReporter.R
0872fabcb328e5b1f7860d9dba9843f7 *R/SpatialRowColumnNormalization.R
851742b37d6571c776417c25a6ed6e74 *R/Transform.R
5104707a080e86d80f476d0b19cc417d *R/TransformReport.R
3a3a7f246de9889998c23b89394a3467 *R/UflSnpInformation.R
7dac249d5533374c9d3ae188a1e186e7 *R/UgpGenomeInformation.R
ca7479f911c6d59a61d6f6425b711a03 *R/UnitModel.R
4446fc2fcb7bcc6aa8c08d8145fae80d *R/UnitModel.fitCnProbes.R
92748cf93ae20ffe6b2696822b708ee9 *R/UnitTypeScaleNormalization.R
474d542259a034cb9cf3abfd8f58bb55 *R/WeightsFile.R
55a5fa0e3566fa5195ef4bbec7ec762a *R/WeightsSet.R
2b421c0f599c3c197b66d85f7398167a *R/bpmapCluster2Cdf.R
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