7dce5404681ecf345a9317bcc2b9e13c *DESCRIPTION
e6d3f7ea06ff077f528d568a9cdd8125 *NAMESPACE
9400b3c4ffcd01c344a61387d7131750 *R/000.R
b6d1bef5586736c914f5336ef1f08e1a *R/006.fixVarArgs.R
2a24a1b15b475dc13ee7aacdde3e0b77 *R/009.setup.R
d0c896db794f2a9c3b5bd6a0211dd85a *R/999.AromaAffymetrix.R
2df9d6a4f9884d569854719ce9b80052 *R/999.DEPRECATED.R
ae5c7a6c9cd6ac16c5192b8acb930e5d *R/999.NonDocumentedObjects.R
0225dc84810194f393299d924596406a *R/999.package.R
c499bbe1c8e3e38fd1b3f1cd90b1e50c *R/ASCRMAv2.R
877ac8074e9bc4aa38bfd97231c4eef3 *R/AbstractProbeSequenceNormalization.R
b2b5dff5b713c83575a7b2254d87f992 *R/AdditiveCovariatesNormalization.R
662fecb270ac1a63af7dca52e7a963c2 *R/AffineCnPlm.R
9fdf2300b76073b1b173bf27323b24a3 *R/AffinePlm.R
302bb9c345b292b058453e84a51afe21 *R/AffineSnpPlm.R
bd12b2e905523e2f7bed310f5ded4b37 *R/AffyGenePDInfo.writeCdf.R
9d3b3364031b8a044ccf1fe07d3d1142 *R/AffymetrixAptSummaryFile.R
4f46c45eec9bcca28dc7c03596dcac20 *R/AffymetrixCdfFile.COUNTS.R
c37a7d5547ca1aea3319d2fc69d0472c *R/AffymetrixCdfFile.MONOCELL.R
eb0d862f92be07f3a63df33217a3af6a *R/AffymetrixCdfFile.PLOT.R
1059341be7963f3868bdcc6c43ceb768 *R/AffymetrixCdfFile.R
b1b2462faad4542b6091ca92310e1abc *R/AffymetrixCdfFile.SNPs.R
43bc37da6e711fac80da5a1881663315 *R/AffymetrixCdfFile.UNIQUE.R
bfd5ab839269ed3480a46d8eaab7770f *R/AffymetrixCdfFile.computeAffinities.R
5baa87d6e225d48f5918f8285dbb6783 *R/AffymetrixCdfFile.getAlleleCellPairs.R
0eaf67877625de4b79be5fbbf4a6a8d3 *R/AffymetrixCdfFile.getAlleleProbePairs.R
d3301c926e84d40fb1564c294c9721ed *R/AffymetrixCdfFile.getAlleleProbePairs2.R
37b576d5236cdec641d3284c835a829d *R/AffymetrixCdfFile.getAlleleProbePairs3.R
83072c75885a25b56d66d32e5db0546b *R/AffymetrixCdfFile.getCellQuartets.R
bc92dacf16d7f61b511d50ebcadb2796 *R/AffymetrixCdfFile.getProbeSequenceData.R
405f1c7144072ee626f9f8f57f5853be *R/AffymetrixCdfFile.getSubsetOfCellIndices.R
6ff15d927e6e5f9c0c32337cb07f8aec *R/AffymetrixCdfFile.getSubsetOfUnits.R
85538edbb401b0814a65a1c3f11776ff *R/AffymetrixCdfFile.getUnitGroupCellMap.R
f0a44546838e2409e94e638881699863 *R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R
5bf4fd73e65a98804043aeb7534a449e *R/AffymetrixCdfFile.groupUnitsByDimension.R
b6358105e28866ab6b80ae3ea870387a *R/AffymetrixCdfFile.readDataFrame.R
cbec6190849ddc83b9f518a6213202e3 *R/AffymetrixCdfFile.writeCdfByExcludingCells.R
eda7f78d7fdfede954d310471a19d7a4 *R/AffymetrixCelFile.BG.R
37025e4a4307aa21c14e44d687e4d4dd *R/AffymetrixCelFile.PLOT.R
d54219c051ccd50dcf0e12f003f82787 *R/AffymetrixCelFile.R
ac4af879de192017925a0582514f33f0 *R/AffymetrixCelFile.allocateFromCdf.R
78d2e04d40eced9ea8dbc78ae8a1e81b *R/AffymetrixCelFile.createFrom.R
57a6c85aa4323648eb42209a7cadcd40 *R/AffymetrixCelFile.extractMatrix.R
1d2a893fd8257bc2299f41adccdefe79 *R/AffymetrixCelFile.fitQuantileNormFcn.R
c6825c372f15bcde3a2e954cd25e616a *R/AffymetrixCelFile.normalizeAffine.R
338a49e2171cc44166498d3e8b20345a *R/AffymetrixCelFile.normalizeQuantile.R
568dd536a38705b33f98fbf2849cc110 *R/AffymetrixCelSet.BG.R
0003686758b65be1fd52289ca7e93845 *R/AffymetrixCelSet.NORM.R
dbc8311cbcb6fedbcedcb4547e4dbdb8 *R/AffymetrixCelSet.PLOT.R
02f3697cfd8099374cfbee78676cfcb9 *R/AffymetrixCelSet.R
0d18b242c50b1fec2ceef81dea94de81 *R/AffymetrixCelSet.convertToUnique.R
50fb99a3e606c0ce2a77735dfce83138 *R/AffymetrixCelSet.extractAffyBatch.R
050a53c177cbd434b0ff510b34a3a891 *R/AffymetrixCelSet.extractFeatureSet.R
1872fc5b7d4cbb13cc3292f423df7987 *R/AffymetrixCelSet.extractMatrix.R
0cb10bec1e770a60d63cf828a730ef46 *R/AffymetrixCelSet.getAverageFile.R
9bc2fc3d6737e37a6fb24b6b2d0a1b5f *R/AffymetrixCelSet.importFromDChip.R
ece5e8fa344cf51382f7f22b79cc883f *R/AffymetrixCelSet.justSNPRMA.R
403cef133d664a24e1a4dcb27f9a9671 *R/AffymetrixCelSet.writeSgr.R
aad66c9efa5a0e9f2744a2b97a27a58b *R/AffymetrixCelSetReporter.R
c21f49557fc26afca772d809e4d8f973 *R/AffymetrixCelSetTuple.R
4b6558e53f106be325e04a63221b0009 *R/AffymetrixCnChpFile.R
f9e1b9e3f5e27becd3931b0e4cad354a *R/AffymetrixCnChpSet.R
edb2c6ffaa19837ea9a93776dad7a599 *R/AffymetrixCnChpSet.extras.R
241911b539f350a3466905f59cdad8b8 *R/AffymetrixCsvFile.R
d2362c5a509a9c5da557b087379fa545 *R/AffymetrixCsvGenomeInformation.R
76b78dc4df66bf782e3b60d28dd0dcc1 *R/AffymetrixFile.R
a2d41c3aca9a2d2362816ddd3e6420b6 *R/AffymetrixFileSet.R
9daa660e9ab06235c2b92b4fe64f8883 *R/AffymetrixFileSet.getIdentifier.R
22a40b6b1c27bbaf459b7a043a1918b0 *R/AffymetrixFileSetReporter.R
6a359585b2617f0ca4bb1b2fa7d34730 *R/AffymetrixNetAffxCsvFile.R
05d3fd51717d57099b7727e6e182ca62 *R/AffymetrixNetAffxCsvFile.XTRS.R
626a296b9b02344c061c1326407dfc17 *R/AffymetrixPgfFile.R
ded561fb8f66c729df252452bea645dd *R/AffymetrixPlatform.R
5a0b15f82035d010986fc002ff7fd222 *R/AffymetrixProbeTabFile.R
17492538f44aa5596275cfdc1738f440 *R/AffymetrixTabularFile.R
edba22732e8dd2cc44b2fec289173d96 *R/AffymetrixTsvFile.R
8b610139a93047d350b90c5c83cb4874 *R/AlleleSummation.R
e1b52cc0298380d1a8f4a175cbfe7c4e *R/AllelicCrosstalkCalibration.PLOT.R
e0d1bd92702ecd33bf8e2930ad43b5e7 *R/AllelicCrosstalkCalibration.R
0a66118acf349aea6f205943b488b49e *R/AllelicCrosstalkCalibration.getSetsOfProbes.R
a18f03a2134aca39169a191bfc2da067 *R/AromaCellCpgFile.AFFX.R
dd6c5343a0e54dd1076bc6a4ec798176 *R/AromaCellMatchScoreFile.AFFX.R
22833ce19e8d15afff48ca88b5372062 *R/AromaCellMatchScoreFile.R
7e2207ac8155eed5223b2c5a63c506bd *R/AromaCellMatchScoreFile.importFromBpmap.R
42e9f6cee2c0c24bfed9cfa5db00bf2e *R/AromaCellPositionFile.AFFX.R
79a7c675c2cef6de74065939cc1fac23 *R/AromaCellSequenceFile.AFFX.R
0f445e7a2de2cb61e4218d0d927eee44 *R/AromaCellSequenceFile.importFromBpmap.R
b39c0b0756771af7c1c32e6bbac8dd70 *R/AromaChipTypeAnnotationFile.R
d59d8a6199e6b8469303fe8f4aec457a *R/AromaPipeline.R
8286f40fc19852609e5be98f59b61d3e *R/AromaUfcFile.R
25055851f8b8c59e897e79613e6fcc92 *R/AromaUflFile.AFFX.R
93a8c12b40a22f7ebcf2843a8654da63 *R/AromaUgpFile.AFFX.R
6da2873bb015f5c36efe193cce4168c9 *R/AromaUnitGcContentFile.AFFX.R
f73b0d2cbcf27a46a55bb78e72e1bc28 *R/AromaUnitTabularBinaryFile.AFFX.PLOT.R
9904dd336758511cabca9ede4c3e56f9 *R/AromaUnitTabularBinaryFile.AFFX.R
fb0c5b7dea630ef8886c0d7e8b48a798 *R/ArrayExplorer.R
d964ed7bb0f0a0ba7b978361e1a719be *R/AvgCnPlm.R
bfb01c72a718b90dda737ae2081ef33a *R/AvgPlm.R
2db2a0e0b972fc77abda390e3cea585e *R/AvgSnpPlm.R
cf80b9ffcb7b246c57537741dc13d4bb *R/BackgroundCorrection.R
c054bd62c8b1d5b8dc54ae4c086e36a9 *R/BaseCountNormalization.R
a806a49b4a8ccad9d5e489e9dc21a103 *R/BasePositionNormalization.R
c3fe3731e4ca983f5a3c1ab53ac85b63 *R/BasePositionNormalization.getFit.R
dba1eff39434a278a70dec07bcbbabee *R/ChipEffectFile.R
bd0dc693e1d93f3eb8a5451cfc057651 *R/ChipEffectFile.TOFULL.R
8354315fd5473f89b90013897f343501 *R/ChipEffectFile.extractTheta.R
2be7311f5db756474804fa9ef943d7a2 *R/ChipEffectFile.fromDataFile.R
02a9ddffb4d6208601e1782c5c89a466 *R/ChipEffectFile.getUnitGroupCellMatrixMap.R
6a96a795391b4fd5546ecd721d50c23f *R/ChipEffectFile.xam.R
090d65de6aa80db68111ce92db129493 *R/ChipEffectGroupMerge.R
0c5330f0e9f7131c74bd10689ea097e5 *R/ChipEffectNnn.extractChromosomalDataFrame.R
d027b9de734a5b5f45a0c2ff5cf56750 *R/ChipEffectSet.PLOT.R
5f49848399a51ce8781d694850ba60ca *R/ChipEffectSet.R
560806f868fc84d8353d9051536015ca *R/ChipEffectSet.STATS.R
223696f2a3644ec3aa0469e745a28612 *R/ChipEffectSet.TOFULL.R
7ad0db18b8fc22f334d5953fe93b7718 *R/ChipEffectSet.calculateBaseline.R
ed8bea002d491047a0d115ad197b3303 *R/ChipEffectSet.extractExpressionSet.R
abeb43793bac7d1d80bd9399072d6ac8 *R/ChipEffectSet.extractTheta.R
6661cdef8f95e25d3968154bf68989af *R/ChipEffectSet.getBaseline.R
b7a3d1a66afcf0df656dd16409f7f1a3 *R/ChipEffectSet.xam.R
45c95eb30f815da0add6f5c25bfe1f2d *R/ChipEffectSetTuple.R
e46c4b7eedf50fce80356c9e4903d499 *R/ChipEffectTransform.R
058de468d5c96289ba0040a837b5469e *R/ChromosomalModel.AFFX.R
15486590e9049c21009845336a22a507 *R/ChromosomalModel.getPositionChipTypeUnit.R
4fed875c451c1394ee96f57bcaf4bc59 *R/ChromosomalModel.getXTheta.R
d1661055cf4c9ab9ff6234bb8bfc2b0c *R/CnChipEffectFile.R
b871fa6332428e3c8bf5a126ebe0e06a *R/CnChipEffectFile.exportAromaSignalBinaryFileList.R
552115ab4bf6d6eed49375c69b0ab912 *R/CnChipEffectSet.R
dc472030aacb5bfa7ed22d659c02b596 *R/CnChipEffectSet.importFromApt.R
1a0393fffa06f65c9bbabcdefa6d51bd *R/CnChipEffectSet.importFromDChip.R
dd1f3aa432496c87fadc6cc374e0ae4f *R/CnChipEffectSet.writeWig.R
885557e308583eab6b5790f8bfe215a7 *R/CnChipEffectSetTuple.R
715ae5520373360b3baf64c0a9d95c4c *R/CnPlm.R
5129350dd39de4b87d9d955cc3323584 *R/CnProbeAffinityFile.R
3bb1f9ddb0596c5819679bd28d323711 *R/CnagCfhFile.R
b86d7a9d4dbc2600db48db8ea5566306 *R/CnagCfhSet.R
4eb311c030adadc31725d196d85ff148 *R/CopyNumberChromosomalModel.applyCCF.R
f4abcae38c717d35434d49b3b9b154ed *R/CopyNumberSegmentationModel.migrateTool.R
9a1610a5e06835bb9ffed26be8a276bc *R/CrlmmModel.EXT.R
3e2543cdc3515abf22e82e990e321ce4 *R/CrlmmModel.R
4d6f34f1f5505d906a7faac387a37bbf *R/CrlmmParametersFile.R
d8b5fa2c52f7d71e87dac5b09d8992fb *R/CrlmmParametersSet.R
8c54962900601fa4564660474b3974f3 *R/DChipCdfBinFile.R
9449523da7357c4438a9fdc5235397a8 *R/DChipCdfBinFile.mapToUnitNamesFile.R
07cd9ffbb90b3471e7c5a36c91c0d674 *R/DChipDcpFile.R
48352a8097850a74fd72402ca259c0c9 *R/DChipDcpSet.R
bbd7fd37addd4f2f6382c434ece5ee7a *R/DChipDcpSet.extras.R
e7a3143dd56d5bcfba04af41ec046014 *R/DChipGenomeInformation.R
47e77356ac7c194a1b228cfebf4c2b02 *R/DChipQuantileNormalization.R
73a80f0f5c7e5911202c7b4ccf565446 *R/DChipSnpInformation.R
bfe2eb3d53893b6f0d357c14a2764afa *R/ExonChipEffectFile.R
52b39f29e5e4ea2031c74bf5c62cf082 *R/ExonChipEffectSet.R
92255be98fb194b53fa7f61ae01f0082 *R/ExonProbeAffinityFile.R
48e09730e9aaba3ad1dfa6d095c70c14 *R/ExonRmaPlm.R
12ac3acc407e19064f251e74e8f34279 *R/ExonRmaPlm.calculateWeights.R
8320da4cbe73f852aa79fe2585417279 *R/FirmaFile.R
94e87308932a8046bd9323fd262745b8 *R/FirmaModel.R
063a915a7e69cd6961379f374fb9bae0 *R/FirmaSet.R
354356eebb0ff24cd77fc4bbcc9eb259 *R/FragmentEquivalentClassNormalization.R
c6ecdf0064f278ca619860f4f908a3e8 *R/FragmentLengthNormalization.R
0fa8dd28072df77edfe28a4f84b10395 *R/GcContentNormalization.R
a93402fd96d8ec5971664458318a5c1a *R/GcContentNormalization2.R
d5d1f698c6e42ef828091656deae070d *R/GcContentNormalization2.plotCovariateEffects.R
f4576044c6beea2971e4b070b82adb8e *R/GcRmaBackgroundCorrection.R
eef9efe5b861e8dc23e559bb902146c7 *R/GenericReporter.R
4bae2dc2451069ed61e28a3f53304bcb *R/GenomeInformation.AFFX.R
7d38c115eccc3d134c263b90890ce599 *R/GenomeInformation.R
1362b6432c95cabaaf90da3496a31e3a *R/HetLogAddCnPlm.R
baba0451573065d544fd1813e93d6ddf *R/HetLogAddPlm.R
6b4c40c760a688738b390cf8b24b8ffb *R/HetLogAddSnpPlm.R
4b4754980638b4612ba90db0bc1825dc *R/LimmaBackgroundCorrection.R
1dc087f307bc8b73ba9cf3d2b2f1415a *R/LinearModelProbeSequenceNormalization.R
c7ab5ce6e08333887ccadefd361307ca *R/MatNormalization.R
979609e48f5977d386b2270f001391ad *R/MatSmoothing.R
ab8305a6d637586411d3fe1300a8d2ca *R/MbeiCnPlm.R
03333fb6e2839534dc4a0b604b98a33f *R/MbeiPlm.R
98a9e5b2dd5639daa0c685bd62956101 *R/MbeiSnpPlm.R
8c69b129d840fa43b3c1760b04b09e3c *R/Model.R
79dc16f4a6e04258834b6cfe045c3b7c *R/MultiArrayUnitModel.R
06bdfacf4606480b7a1abbd35cb50e60 *R/NormExpBackgroundCorrection.R
9425a82d15549ab70d3a101035c79320 *R/OpticalBackgroundCorrection.R
9388086af14d2145806a908149b6fa41 *R/Package.XTRA.R
0ab959ab5da28d699c2198f5fc454ec4 *R/ParameterCelFile.R
1cfaa8cdd610af51dfbdf096fe58e6f8 *R/ParameterCelFile.extractNnn.R
b34efcd98f55ff9b3180d2fc82735b63 *R/ParameterCelSet.R
03c837d26e497acb0f9aae70e5b94ad8 *R/ProbeAffinityFile.R
e17249275cd130c8c3151d169891c176 *R/ProbeLevelModel.R
57e3f3df71ab31ef684e1ec2c9df15ba *R/ProbeLevelModel.calculateResiduals.R
0d3b397af6860b378ba45094c630f2fd *R/ProbeLevelModel.calculateWeights.R
26b25976a55b1736f4008a559e0d6ce1 *R/ProbeLevelModel.fit.R
f5d3a745926e64fe5914e9056a115d09 *R/ProbeLevelTransform.R
f87fa5ce10af3de5fc13113f34ef8d22 *R/ProbeLevelTransform3.R
8d1951f9b492d596751cd437aac47338 *R/QualityAssessmentFile.R
5980413044ffc7f9a16a4179ec3fa55c *R/QualityAssessmentModel.R
cd4ad27696391d0cfc86c36240380680 *R/QualityAssessmentSet.R
39500c3ae1dbbbdd29ba886cb6ddedaa *R/QuantileNormalization.R
2aef804fc3eb92f45bbcbf24cb3d6b22 *R/QuantileNormalization.xtra.R
e26f5b7f291d9706512fc195abdc7553 *R/ReseqCrosstalkCalibration.R
b5d9d0e1c6803d9ca8a1c24e6b8497f0 *R/ResidualFile.R
92eee0f107d6e265b39c8ce2d50d4661 *R/ResidualSet.R
43d0dd6e0e652b6ff04e95fa74a1f1bd *R/RmaBackgroundCorrection.R
ecf7f6b7c504251449179102670a4ddc *R/RmaCnPlm.R
a597c09fd6988fef7e32d483090f3332 *R/RmaPlm.R
122aa7007404368602d3918000c0f6e3 *R/RmaSnpPlm.R
975987e5a7969f08906c3e4dfe6eb1ea *R/ScaleNormalization.R
f55b9e0f50b50bae3e4be5f3e88cc84b *R/ScaleNormalization3.R
a44d54d8c355a346fc861fd57155cc3b *R/SingleArrayUnitModel.R
7bd66e4ce257100ed5b05d1fc05193eb *R/SingleArrayUnitModel.fit.R
e5aac582b57d0b59dc2dda93ed3657f6 *R/SmoothMultiarrayModel.R
aff60a3290638a75822fa6ccedd76c4a *R/SmoothMultiarrayModel.fit.R
8415a030c231c59f069313f2ade43851 *R/SmoothRmaModel.R
271a88f24f0d8d421b99539576488f5d *R/SmoothSaModel.R
903096b3edacd58a14fd4e56b6ef2fc2 *R/SnpChipEffectFile.R
3a08a62c64ca1b5e5741f85bd0e39faa *R/SnpChipEffectFile.exportTotalAndFracB.R
5b650f2d9a6451d8ef3d9e739858f637 *R/SnpChipEffectFile.extractTotalAndFracB.R
464864cd959b63f701adf763361491d5 *R/SnpChipEffectGroupMerge.R
11f11d6eab9f712dc550deaacd2ce078 *R/SnpChipEffectNnn.extractCNT.R
4b293ddf9d932ba346084863ba10f2a8 *R/SnpChipEffectNnn.writeCNT.R
c763a234bec1d976a712390117f3c4a9 *R/SnpChipEffectSet.R
cf38bbbf61c6cf75be6b1ea128e6534e *R/SnpChipEffectSet.exportTotalAndFracB.R
2e60649c9b10ade584186facfdb9e923 *R/SnpChipEffectSet.extractAlleleSet.R
db5c17fb23bb0634dc4b71fa4ea74eff *R/SnpChipEffectSet.extractSnpCnvQSet.R
a8d4bc3f9eee98dffd7cda4adf46f30c *R/SnpChipEffectSet.extractSnpQSet.R
6164646e3d852812fc1f1530b6c7f35c *R/SnpChipEffectSet.extractTotalAndFreqB.R
e41da8d1cac0535636736be4821751b6 *R/SnpCnvQSet.extractTheta.R
ab45359aa75ed6dcf26529b4e3e02270 *R/SnpInformation.R
6ffa988e44e1411af39d304bb61f43d8 *R/SnpPlm.R
d213197b1c17a09b45abf7c13d59bd7f *R/SnpProbeAffinityFile.R
bf5f30204865b2ddd14564a9efb4ed49 *R/SnpQSet.extractTheta.R
95dd232e3cbe7ff8334d8ef6c79a3797 *R/SpatialReporter.R
399883769badda469e933a3a0f2a6a2d *R/SpatialRowColumnNormalization.R
790a367320e8621a09e4b50c718078fc *R/Transform.R
81ad6be6c4cdde7105d2be65f9c9f2e8 *R/TransformReport.R
dee8e1f1478cde2fd6a6bdee240505ff *R/UflSnpInformation.R
493450212e39eb374f38f07d5ecddd2c *R/UgpGenomeInformation.R
03079a9c0f419d7e86cf43c5493bb495 *R/UnitModel.R
736377b15a86c55d0fb4c905c5551f4f *R/UnitModel.fitCnProbes.R
9660ded9bebd2af094ea8dd5a1972acc *R/UnitTypeScaleNormalization.R
867f384237d0c263cbb58051f765e57f *R/WeightsFile.R
359bff0161bdd5f739a902679aaef985 *R/WeightsSet.R
f0c12359f57d7954f4ecc813ddf27053 *R/bpmapCluster2Cdf.R
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