bfcf584a88d00a1292f81c6790cb661e *DESCRIPTION
000c5c402a3ed43f962761ae38508a66 *NAMESPACE
432b6f8b8eae19be73b7f067afb82438 *NEWS
4bcbb5139128447d6309d89980703e1c *R/000.R
b6d1bef5586736c914f5336ef1f08e1a *R/006.fixVarArgs.R
ee7af24de9e03e26b18ae820ff0c196b *R/009.setup.R
805a07eddfd4ae30baec1683fd3a1927 *R/021.dynamic_imports.R
6ad90c6d9ec62a231044e22f540dfee0 *R/999.AromaAffymetrix.R
3a0bb9c9f5a3aeb42ceeaa7e7abc7a6f *R/999.DEPRECATED.R
ae5c7a6c9cd6ac16c5192b8acb930e5d *R/999.NonDocumentedObjects.R
b28f6061a61060fd492c3718a752adf1 *R/999.package.R
c499bbe1c8e3e38fd1b3f1cd90b1e50c *R/ASCRMAv2.R
1e5cfeaa9d44ee2d59c8d745fbd1d9ae *R/AbstractProbeSequenceNormalization.R
ef48df37f5eecee740d54ee9bdac413e *R/AdditiveCovariatesNormalization.R
662fecb270ac1a63af7dca52e7a963c2 *R/AffineCnPlm.R
5b5a363b1bfeb16d1db14b287a86258e *R/AffinePlm.R
302bb9c345b292b058453e84a51afe21 *R/AffineSnpPlm.R
ecdfb12676a964b4fefc484278204be9 *R/AffyGenePDInfo.writeCdf.R
9d3b3364031b8a044ccf1fe07d3d1142 *R/AffymetrixAptSummaryFile.R
251a5b4a05b7855b7d0ebb5aefa8ac60 *R/AffymetrixCdfFile.COUNTS.R
0a25fbdac3cda0dd0638c24391fc372c *R/AffymetrixCdfFile.MONOCELL.R
989ae5120f4acf23a8b9811e77bfbe2f *R/AffymetrixCdfFile.PLOT.R
3264a500966014aaf6c00a83ef450791 *R/AffymetrixCdfFile.R
b1b2462faad4542b6091ca92310e1abc *R/AffymetrixCdfFile.SNPs.R
46a59869aa23eb42ef94e74609d0b498 *R/AffymetrixCdfFile.UNIQUE.R
e9b258124c1e48eb6d36e8e6208763a3 *R/AffymetrixCdfFile.computeAffinities.R
c86d81dba553932578116cd70b0ab8c0 *R/AffymetrixCdfFile.getAlleleCellPairs.R
b93b6d649abf583d2522d2b73d9d2368 *R/AffymetrixCdfFile.getAlleleProbePairs.R
be95acbc392f9f739f836c1b1d6642cb *R/AffymetrixCdfFile.getAlleleProbePairs2.R
c80566876222f8ad00b41c570bb6a2ce *R/AffymetrixCdfFile.getAlleleProbePairs3.R
bfc771566776923af42c9950f9c7594f *R/AffymetrixCdfFile.getCellQuartets.R
3df315c0ecd78932cbee3f4907481e4c *R/AffymetrixCdfFile.getProbeSequenceData.R
baaf8088b9cdb9b8800b6ce9c8b3eabb *R/AffymetrixCdfFile.getSubsetOfCellIndices.R
24bd1a4c00875aecd57b201d657d37ad *R/AffymetrixCdfFile.getSubsetOfUnits.R
383a32b18a6a476ee2c72ab23221e4c4 *R/AffymetrixCdfFile.getUnitGroupCellMap.R
dcbffca4285dc229c34ad6fc3b36bcb3 *R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R
5bf4fd73e65a98804043aeb7534a449e *R/AffymetrixCdfFile.groupUnitsByDimension.R
e5d2cc9bfb57e55b2e162bb7e2b3cfd1 *R/AffymetrixCdfFile.readDataFrame.R
22e0c3e3fb984e26917c68e183813b44 *R/AffymetrixCdfFile.writeCdfByExcludingCells.R
1b2ae008fa7e7ee4a1f042ee77ba671c *R/AffymetrixCelFile.BG.R
9d78e45cc9dcbf6f9db2ab6cfa5931f4 *R/AffymetrixCelFile.PLOT.R
bc5108e8dcd0ab8d0f0a8921358e39b5 *R/AffymetrixCelFile.R
bd9ca3ac52de6ab85f11b5c0f0f336bb *R/AffymetrixCelFile.allocateFromCdf.R
62ece176540b8bbaa371adc2cb0bcbc5 *R/AffymetrixCelFile.createFrom.R
3b7732b5cdfe3a551e6063166cf9a8ae *R/AffymetrixCelFile.extractMatrix.R
1d2a893fd8257bc2299f41adccdefe79 *R/AffymetrixCelFile.fitQuantileNormFcn.R
99dc3cbe0674ce2c2178ff309f19f708 *R/AffymetrixCelFile.normalizeAffine.R
77d15f6bbdfdf14fb992e5c694c24501 *R/AffymetrixCelFile.normalizeQuantile.R
219fab7ad1e8652654069a58e286a641 *R/AffymetrixCelSet.BG.R
776a4a77dd31b2c0116e3d39dc3edee3 *R/AffymetrixCelSet.NORM.R
836190e5c9852b10494f449c1f9ae199 *R/AffymetrixCelSet.PLOT.R
1211b8fa437beb684dd1fb3604569c4b *R/AffymetrixCelSet.R
a02477f1186737e12cbea54d60ed0c7e *R/AffymetrixCelSet.convertToUnique.R
2a5b592ebd4cc236a0fc5d77a6c4f704 *R/AffymetrixCelSet.extractAffyBatch.R
008d86ddfd3f64ce1006c63f43941ce9 *R/AffymetrixCelSet.extractFeatureSet.R
79a7a5b4829c4b9096bf2780e4c96798 *R/AffymetrixCelSet.extractMatrix.R
28bf4a23f4521a7016cb41c00a5f122b *R/AffymetrixCelSet.getAverageFile.R
d2513610b00e6563b37698fe70be2bd8 *R/AffymetrixCelSet.importFromDChip.R
87b7abc2139a8e3bbef7051fcc23e136 *R/AffymetrixCelSet.justSNPRMA.R
bd57c24f7470da248dec0e040e429dd3 *R/AffymetrixCelSet.writeSgr.R
bb1aac0f8318d0cb670dbafc852fc951 *R/AffymetrixCelSetReporter.R
ad71e397fe6314b88c5a691f904d3be8 *R/AffymetrixCelSetTuple.R
20b3ec197a3a1830ed1c90b3e49ed999 *R/AffymetrixCnChpFile.R
3ba0cc8b62879d09ed6e976ca87458b6 *R/AffymetrixCnChpSet.R
8c92585b60da38d3537bc4266d5cf3bc *R/AffymetrixCnChpSet.extras.R
241911b539f350a3466905f59cdad8b8 *R/AffymetrixCsvFile.R
5236ddc4157a6234e38c0f6c421ba03d *R/AffymetrixCsvGenomeInformation.R
76b78dc4df66bf782e3b60d28dd0dcc1 *R/AffymetrixFile.R
dad81031df1f7cc3495c61900e939437 *R/AffymetrixFileSet.R
8d83539dae49e1faf42ef4a8e2966bca *R/AffymetrixFileSet.getIdentifier.R
22a40b6b1c27bbaf459b7a043a1918b0 *R/AffymetrixFileSetReporter.R
409ef85f3364000241a0f9084e8a6cf6 *R/AffymetrixNetAffxCsvFile.R
05d3fd51717d57099b7727e6e182ca62 *R/AffymetrixNetAffxCsvFile.XTRS.R
efd24cc11b2dc6256fee2173f943192f *R/AffymetrixPgfFile.R
ded561fb8f66c729df252452bea645dd *R/AffymetrixPlatform.R
b42ac548be0f039ee19290deaa8170ef *R/AffymetrixProbeTabFile.R
17492538f44aa5596275cfdc1738f440 *R/AffymetrixTabularFile.R
f1b4cd253d17cfbffbf00b931f2095db *R/AffymetrixTsvFile.R
dbb895c4c702ac60b86196a45af08eac *R/AlleleSummation.R
ead56362ebbe0966957b4169878bf53f *R/AllelicCrosstalkCalibration.PLOT.R
25bd15211061795c8d97a1695450c6bf *R/AllelicCrosstalkCalibration.R
6f50d83a1cb4c7c466637a5ec7c9821f *R/AllelicCrosstalkCalibration.getSetsOfProbes.R
a18f03a2134aca39169a191bfc2da067 *R/AromaCellCpgFile.AFFX.R
dd6c5343a0e54dd1076bc6a4ec798176 *R/AromaCellMatchScoreFile.AFFX.R
22833ce19e8d15afff48ca88b5372062 *R/AromaCellMatchScoreFile.R
47be87dbda950d59be909896c4ebc846 *R/AromaCellMatchScoreFile.importFromBpmap.R
42e9f6cee2c0c24bfed9cfa5db00bf2e *R/AromaCellPositionFile.AFFX.R
79a7c675c2cef6de74065939cc1fac23 *R/AromaCellSequenceFile.AFFX.R
d23eeff0dd730406ceaad0866c9c1b55 *R/AromaCellSequenceFile.importFromBpmap.R
9f0924bd136576f66b834db069e73e19 *R/AromaChipTypeAnnotationFile.R
d59d8a6199e6b8469303fe8f4aec457a *R/AromaPipeline.R
46eb0c1989730db980afd5d22c4d57c4 *R/AromaUfcFile.R
25055851f8b8c59e897e79613e6fcc92 *R/AromaUflFile.AFFX.R
93a8c12b40a22f7ebcf2843a8654da63 *R/AromaUgpFile.AFFX.R
6da2873bb015f5c36efe193cce4168c9 *R/AromaUnitGcContentFile.AFFX.R
04da6069472ff4ef9f94350b54fcb271 *R/AromaUnitTabularBinaryFile.AFFX.PLOT.R
9904dd336758511cabca9ede4c3e56f9 *R/AromaUnitTabularBinaryFile.AFFX.R
847fc281c6ac7f68db23c905fa66c8e1 *R/ArrayExplorer.R
d964ed7bb0f0a0ba7b978361e1a719be *R/AvgCnPlm.R
e7619d3e67f282d7af6b6e3ca7135d3b *R/AvgPlm.R
2db2a0e0b972fc77abda390e3cea585e *R/AvgSnpPlm.R
cf80b9ffcb7b246c57537741dc13d4bb *R/BackgroundCorrection.R
8724235090dbe56880e7173d4191f85a *R/BaseCountNormalization.R
88df467a43ec6f71ac0e351b84b1674a *R/BasePositionNormalization.R
ad22c0e9d6630defae357e03b6c46b95 *R/BasePositionNormalization.getFit.R
dda050d631755a6b732c2d21a351ab7a *R/ChipEffectFile.R
9c31c5e3fe25135d60e6f846d6ac2c0e *R/ChipEffectFile.TOFULL.R
8354315fd5473f89b90013897f343501 *R/ChipEffectFile.extractTheta.R
8b94828f0feefc6290e3b5afbfc5a953 *R/ChipEffectFile.fromDataFile.R
02a9ddffb4d6208601e1782c5c89a466 *R/ChipEffectFile.getUnitGroupCellMatrixMap.R
6a96a795391b4fd5546ecd721d50c23f *R/ChipEffectFile.xam.R
042bebd527cca9a787668770a58c4f29 *R/ChipEffectGroupMerge.R
50ef26c9629e7dd9abb6f6137d3ac22d *R/ChipEffectNnn.extractChromosomalDataFrame.R
d027b9de734a5b5f45a0c2ff5cf56750 *R/ChipEffectSet.PLOT.R
b6741c787a5df3e52572b2ff1c2010b2 *R/ChipEffectSet.R
dd4ad040b79cdad4c8af80aae65aad11 *R/ChipEffectSet.STATS.R
63a5a603e07200c7f37cce98f6ac70fa *R/ChipEffectSet.TOFULL.R
ce903b5346caf1c4d87f460e0814274f *R/ChipEffectSet.calculateBaseline.R
6cefc2a12fb776e8f72945638a3c783c *R/ChipEffectSet.extractExpressionSet.R
27bc89f3898e27032f1164e8f91aca44 *R/ChipEffectSet.extractTheta.R
a5646fb6e1ef68c381be9c4209447db9 *R/ChipEffectSet.getBaseline.R
c71923cd7aae6c838e52e22a42b71526 *R/ChipEffectSet.xam.R
45c95eb30f815da0add6f5c25bfe1f2d *R/ChipEffectSetTuple.R
e46c4b7eedf50fce80356c9e4903d499 *R/ChipEffectTransform.R
058de468d5c96289ba0040a837b5469e *R/ChromosomalModel.AFFX.R
df5745886c74ac52a17e62ae51821296 *R/ChromosomalModel.getPositionChipTypeUnit.R
4fed875c451c1394ee96f57bcaf4bc59 *R/ChromosomalModel.getXTheta.R
7b256e72139a4ace4024a40f4510bc06 *R/CnChipEffectFile.R
b871fa6332428e3c8bf5a126ebe0e06a *R/CnChipEffectFile.exportAromaSignalBinaryFileList.R
2ce5364fcad1f05084a2079cab8edfef *R/CnChipEffectSet.R
de9e0b2d95ca4010584bead835c42853 *R/CnChipEffectSet.importFromApt.R
cc5a0b9346858101a4a4325efee34e41 *R/CnChipEffectSet.importFromDChip.R
fe5a7a6dfecd586a77b071a5b7ac60df *R/CnChipEffectSet.writeWig.R
885557e308583eab6b5790f8bfe215a7 *R/CnChipEffectSetTuple.R
24d84efc48dafb3fec020afa77832294 *R/CnPlm.R
e3b9f210fea2f2489c1a423ab90a1847 *R/CnProbeAffinityFile.R
f1b629c3d86134ab6ab3123d3d47eb50 *R/CnagCfhFile.R
ebcb6569a13c6dc99ba7a62edb887ab5 *R/CnagCfhSet.R
465194ef01c336db34a41b09c549274d *R/CopyNumberChromosomalModel.applyCCF.R
f4abcae38c717d35434d49b3b9b154ed *R/CopyNumberSegmentationModel.migrateTool.R
2326cb79143b2c129acfe8f164eb68fb *R/CrlmmModel.EXT.R
b0bbfec89c15379490d099727cc8f4e6 *R/CrlmmModel.R
4d6f34f1f5505d906a7faac387a37bbf *R/CrlmmParametersFile.R
7c4dbc341545a3fe08bb339b8f0c8a2a *R/CrlmmParametersSet.R
02a9113d3e02c14c3317dc5313f5b975 *R/DChipCdfBinFile.R
9449523da7357c4438a9fdc5235397a8 *R/DChipCdfBinFile.mapToUnitNamesFile.R
6141cf179d0a31f97cafa94785d3b7f3 *R/DChipDcpFile.R
47f4a3dcb882b514c98125af86384e0b *R/DChipDcpSet.R
34ac1c0b6e0056267eb62121a7f4652c *R/DChipDcpSet.extras.R
06e67e441eb896de9ae5e14e0aebe1f2 *R/DChipGenomeInformation.R
0e335632be9fce301e97f0ed0874a767 *R/DChipQuantileNormalization.R
dd2a39b58cfe4e41158329074f48c9c1 *R/DChipSnpInformation.R
6e180bb1d51fdd1d2376145336340b0e *R/ExonChipEffectFile.R
8da6db9f361cfeb767b3cc8bf8278f34 *R/ExonChipEffectSet.R
266b92452ab3531f18a057e8186b35bf *R/ExonProbeAffinityFile.R
9e1c16cc1fc6610e4035477a3f509b1f *R/ExonRmaPlm.R
000bd5050f957c298dabf4496d9d9557 *R/ExonRmaPlm.calculateWeights.R
c6c44cab2751719364412943bbcfce29 *R/FirmaFile.R
2d1b6aa989f467eec6fb9ea5e03f97db *R/FirmaModel.R
af23a680e54e1b20a19eb21888843244 *R/FirmaSet.R
d105007f9f15ee7be42815ec4869815a *R/FragmentEquivalentClassNormalization.R
cdfeed0ba4cc32409a56962a0a8b3ffb *R/FragmentLengthNormalization.R
27b5c11796f9f4f292a01339144e8fbf *R/GcContentNormalization.R
a93402fd96d8ec5971664458318a5c1a *R/GcContentNormalization2.R
f62c4ce3b1fb8698481ed104971cc33b *R/GcContentNormalization2.plotCovariateEffects.R
bcae71fdac2b9a5ecbce364ce599ff81 *R/GcRmaBackgroundCorrection.R
6bf466454a9f4858eef48eeea71a8dd3 *R/GenericReporter.R
0e64869b32cc84bdc6690c0742d0825e *R/GenomeInformation.AFFX.R
394380ee8b62d1f1115a9a45e27b8d9b *R/GenomeInformation.R
1362b6432c95cabaaf90da3496a31e3a *R/HetLogAddCnPlm.R
77ef80f6c965d1469629e439b0dba6cd *R/HetLogAddPlm.R
6b4c40c760a688738b390cf8b24b8ffb *R/HetLogAddSnpPlm.R
5a5913ee39251829536982c3d92f573c *R/LimmaBackgroundCorrection.R
1dc087f307bc8b73ba9cf3d2b2f1415a *R/LinearModelProbeSequenceNormalization.R
9a2b55b8999c1b101f0d22228a94b98c *R/MatNormalization.R
4b81a5b664d9226a28f3f3794658dbc7 *R/MatSmoothing.R
ab8305a6d637586411d3fe1300a8d2ca *R/MbeiCnPlm.R
ed033d6421ec019f1fc7f900423fdc3b *R/MbeiPlm.R
98a9e5b2dd5639daa0c685bd62956101 *R/MbeiSnpPlm.R
8f730023d58c71b98e6c352842f1e62a *R/Model.R
51911859d289f74f76199ab1434b62a6 *R/MultiArrayUnitModel.R
06bdfacf4606480b7a1abbd35cb50e60 *R/NormExpBackgroundCorrection.R
a05623beea32667bad30ea5840fc709d *R/OpticalBackgroundCorrection.R
cee1d18c96a8dcb21fe330b1e994767f *R/Package.XTRA.R
cc69db3d5d4b02a092846700b7b719c6 *R/ParameterCelFile.R
1cfaa8cdd610af51dfbdf096fe58e6f8 *R/ParameterCelFile.extractNnn.R
0e3dae908746eead815924d8509abaf2 *R/ParameterCelSet.R
db28366006be48eb6417d35bd1f259cc *R/ProbeAffinityFile.R
e17249275cd130c8c3151d169891c176 *R/ProbeLevelModel.R
ebed1c29ae1afa3dfec3a35bccae7bbd *R/ProbeLevelModel.calculateResiduals.R
0bbca6700ebe491a5f7b9dfd82cc5d20 *R/ProbeLevelModel.calculateWeights.R
696099885e945f818ac8f0d205da1b31 *R/ProbeLevelModel.fit.R
f5d3a745926e64fe5914e9056a115d09 *R/ProbeLevelTransform.R
1b5945cc7164e3bb497ae1fe79c7e5a6 *R/ProbeLevelTransform3.R
1471716da2a53811de47fa231e6c5b15 *R/QualityAssessmentFile.R
1ac0c9274d824b8d4dac2a2995e6ae26 *R/QualityAssessmentModel.R
cd4ad27696391d0cfc86c36240380680 *R/QualityAssessmentSet.R
28b7140db75fddec27525a45285fc12b *R/QuantileNormalization.R
2aef804fc3eb92f45bbcbf24cb3d6b22 *R/QuantileNormalization.xtra.R
860354378dd23777f63b737e17d91db9 *R/ReseqCrosstalkCalibration.R
bd6b23b2a2c3b8a40b17abbd8bd5c9b7 *R/ResidualFile.R
2d3b64b64bf06f6b6a0dfdc456ed6fbe *R/ResidualSet.R
1aa761578da64cec29f8b5d5d7e2a669 *R/RmaBackgroundCorrection.R
ecf7f6b7c504251449179102670a4ddc *R/RmaCnPlm.R
ac6641374dfb18ce108dbd937f683065 *R/RmaPlm.R
122aa7007404368602d3918000c0f6e3 *R/RmaSnpPlm.R
5d2b9ed0e2b3ac8a630dc5c0611f8d38 *R/ScaleNormalization.R
4c8b864f2cac3d5e47c931956074fa62 *R/ScaleNormalization3.R
c6b0e8fdc0856856cf29386cd0876e8a *R/SingleArrayUnitModel.R
7d431bf5033b22f9ab26ac50703c8a5f *R/SingleArrayUnitModel.fit.R
178bcd78049eeb40e249f1c2b20b04e1 *R/SmoothMultiarrayModel.R
f44e74748563ad77507e0afa744f1066 *R/SmoothMultiarrayModel.fit.R
8415a030c231c59f069313f2ade43851 *R/SmoothRmaModel.R
271a88f24f0d8d421b99539576488f5d *R/SmoothSaModel.R
83ea8f584eaec7892e124ab4413aba1f *R/SnpChipEffectFile.R
3a08a62c64ca1b5e5741f85bd0e39faa *R/SnpChipEffectFile.exportTotalAndFracB.R
d2d3b7586e857c9eed5f873089d4ace7 *R/SnpChipEffectFile.extractTotalAndFracB.R
464864cd959b63f701adf763361491d5 *R/SnpChipEffectGroupMerge.R
11f11d6eab9f712dc550deaacd2ce078 *R/SnpChipEffectNnn.extractCNT.R
4b293ddf9d932ba346084863ba10f2a8 *R/SnpChipEffectNnn.writeCNT.R
2108b634b9f6122ffc054a4dffe16033 *R/SnpChipEffectSet.R
b2c5215dbec34716ca24a1296d756fda *R/SnpChipEffectSet.exportTotalAndFracB.R
1444e32f16ffb502fc977f0e3e585f30 *R/SnpChipEffectSet.extractAlleleSet.R
d759c15129055b07d1b8eb491b4b4570 *R/SnpChipEffectSet.extractSnpCnvQSet.R
2dcba4bbb33cba21a21c3bc72f2e9a18 *R/SnpChipEffectSet.extractSnpQSet.R
bc857b9ba29f3ba1fe1c3e5912e844d1 *R/SnpChipEffectSet.extractTotalAndFreqB.R
db95f57d9a491d9059eb1be07ef8b01c *R/SnpCnvQSet.extractTheta.R
e4ed1d6411b1c73ea8b41e08d40dbbd3 *R/SnpInformation.R
401fecb21ee3ee6f4397e44f1ee97ed3 *R/SnpPlm.R
0256c199862503876486455075a7e6e7 *R/SnpProbeAffinityFile.R
37b94dd8917eefab71dc04539758240b *R/SnpQSet.extractTheta.R
92e0e13f81198ff6293a4394f457b6f2 *R/SpatialReporter.R
7b26c7ee1eade219d5e0b5070903237c *R/SpatialRowColumnNormalization.R
84924c271b19fee674e8069a5ef8c255 *R/Transform.R
1b85ef92fde8e862091a29b14fa5b1cb *R/TransformReport.R
3f6f190fa6d2a7d2c3b3913d77df801e *R/UflSnpInformation.R
6342277005582d091f5d234cf7784448 *R/UgpGenomeInformation.R
03079a9c0f419d7e86cf43c5493bb495 *R/UnitModel.R
44627954bf9a70448bec8287f2904271 *R/UnitModel.fitCnProbes.R
81d2704263ac11a57d2c8797ae779518 *R/UnitTypeScaleNormalization.R
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