08de25dcfa241f7bfba7216291a71a2d *DESCRIPTION
73f9645a546038e1992a99cf59017b0c *NAMESPACE
9400b3c4ffcd01c344a61387d7131750 *R/000.R
0be4ad6596832ecb10af9d264585616f *R/006.fixVarArgs.R
dc193ab3c1d3cf0b5cd9400752585fa5 *R/009.setup.R
94bf454cc3e6953b6feb80599602b47e *R/999.AromaAffymetrix.R
9adc1044df0937346d533f54773af11b *R/999.DEPRECATED.R
ae5c7a6c9cd6ac16c5192b8acb930e5d *R/999.NonDocumentedObjects.R
dd700966d66dac6028543f5d4ab067df *R/999.package.R
c499bbe1c8e3e38fd1b3f1cd90b1e50c *R/ASCRMAv2.R
a8b212ada010bafdcce8e45dfe4d1cd1 *R/AbstractProbeSequenceNormalization.R
ab859a8f905b5dcc9b02cd9ae0408352 *R/AdditiveCovariatesNormalization.R
662fecb270ac1a63af7dca52e7a963c2 *R/AffineCnPlm.R
9fdf2300b76073b1b173bf27323b24a3 *R/AffinePlm.R
302bb9c345b292b058453e84a51afe21 *R/AffineSnpPlm.R
4c0482fe72f77c24ac65a06ee64e19ea *R/AffyGenePDInfo.writeCdf.R
9d3b3364031b8a044ccf1fe07d3d1142 *R/AffymetrixAptSummaryFile.R
4f46c45eec9bcca28dc7c03596dcac20 *R/AffymetrixCdfFile.COUNTS.R
9ad647d996cac7c2e2993cc186174bd5 *R/AffymetrixCdfFile.MONOCELL.R
dc999943de6ac6744321ac90c64221c1 *R/AffymetrixCdfFile.PLOT.R
349f70084c5667c232af3c55c06845a6 *R/AffymetrixCdfFile.R
b1b2462faad4542b6091ca92310e1abc *R/AffymetrixCdfFile.SNPs.R
58f5b1efe74aba2d72da3e33cf8afc00 *R/AffymetrixCdfFile.UNIQUE.R
189752f2448a1f86cf94bb122eb3aead *R/AffymetrixCdfFile.computeAffinities.R
877107fe0b9c77d11a01647e1271d46f *R/AffymetrixCdfFile.getAlleleCellPairs.R
d3dd70305d6c1dc63b169a480f2b3fd4 *R/AffymetrixCdfFile.getAlleleProbePairs.R
65f2591f45e0f15c8f20a9506705dfb4 *R/AffymetrixCdfFile.getAlleleProbePairs2.R
5c0afe542e51e45bbe8d21226f1d6800 *R/AffymetrixCdfFile.getAlleleProbePairs3.R
17e1d181a4066b381609e6fe4b7c78d7 *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
2123f9bae84379a054c0c4f230a6b870 *R/AffymetrixCdfFile.groupUnitsByDimension.R
b6358105e28866ab6b80ae3ea870387a *R/AffymetrixCdfFile.readDataFrame.R
60b8a7b1e946aab9ec84ee8e9416be2c *R/AffymetrixCdfFile.writeCdfByExcludingCells.R
6fc2d9de019fdb3840a0ac3f00670595 *R/AffymetrixCelFile.BG.R
37025e4a4307aa21c14e44d687e4d4dd *R/AffymetrixCelFile.PLOT.R
0134e6673fb5cf42280aa2feea32bbe2 *R/AffymetrixCelFile.R
d3d4f92a4926863e33d881d9d7f2442f *R/AffymetrixCelFile.allocateFromCdf.R
2fc7a047532e79dbf2aa9198fb54a842 *R/AffymetrixCelFile.createFrom.R
b2a18bcdece6dc81b42a906fd79e8190 *R/AffymetrixCelFile.extractMatrix.R
1d2a893fd8257bc2299f41adccdefe79 *R/AffymetrixCelFile.fitQuantileNormFcn.R
7b48de212e456e4c415d999fde18f641 *R/AffymetrixCelFile.normalizeAffine.R
c69a51b0f9146475ce8fe5bda0d6e99c *R/AffymetrixCelFile.normalizeQuantile.R
25e66c9aa20c8dc2dd3b1befd242a029 *R/AffymetrixCelSet.BG.R
f7a3de9b47482e89ca84359b50d6410b *R/AffymetrixCelSet.NORM.R
dbc8311cbcb6fedbcedcb4547e4dbdb8 *R/AffymetrixCelSet.PLOT.R
c2aaf6fe14aa4481016e3a5848107748 *R/AffymetrixCelSet.R
d349e241a92a7e2735f1dff09d881539 *R/AffymetrixCelSet.convertToUnique.R
50fb99a3e606c0ce2a77735dfce83138 *R/AffymetrixCelSet.extractAffyBatch.R
050a53c177cbd434b0ff510b34a3a891 *R/AffymetrixCelSet.extractFeatureSet.R
8deea6841e44a96c93f58e20824ad5cc *R/AffymetrixCelSet.extractMatrix.R
de66d16227ed002f4dc5aeb918599bc7 *R/AffymetrixCelSet.getAverageFile.R
d1141301a655fdc4abec5f39c36cbf6d *R/AffymetrixCelSet.importFromDChip.R
95965965985cb783cd643454226bcc64 *R/AffymetrixCelSet.justSNPRMA.R
403cef133d664a24e1a4dcb27f9a9671 *R/AffymetrixCelSet.writeSgr.R
aad66c9efa5a0e9f2744a2b97a27a58b *R/AffymetrixCelSetReporter.R
c21f49557fc26afca772d809e4d8f973 *R/AffymetrixCelSetTuple.R
ec0cd7548ba0274f1b49dbecffccfc35 *R/AffymetrixCnChpFile.R
3b8df0969e9041b816a9221856503e2b *R/AffymetrixCnChpSet.R
dc3daab0d19ef92b3a68b621ba4186cd *R/AffymetrixCnChpSet.extras.R
241911b539f350a3466905f59cdad8b8 *R/AffymetrixCsvFile.R
19e8cc735207216f9f9f5a01a6561712 *R/AffymetrixCsvGenomeInformation.R
76b78dc4df66bf782e3b60d28dd0dcc1 *R/AffymetrixFile.R
a2d41c3aca9a2d2362816ddd3e6420b6 *R/AffymetrixFileSet.R
dc23c4313d3428faa576597ff0ec7d90 *R/AffymetrixFileSet.getIdentifier.R
22a40b6b1c27bbaf459b7a043a1918b0 *R/AffymetrixFileSetReporter.R
4f902850c8feaca9234d4cea93e47214 *R/AffymetrixNetAffxCsvFile.R
05d3fd51717d57099b7727e6e182ca62 *R/AffymetrixNetAffxCsvFile.XTRS.R
626a296b9b02344c061c1326407dfc17 *R/AffymetrixPgfFile.R
ded561fb8f66c729df252452bea645dd *R/AffymetrixPlatform.R
7e62612e6c2120eb09e4b3999aaade12 *R/AffymetrixProbeTabFile.R
17492538f44aa5596275cfdc1738f440 *R/AffymetrixTabularFile.R
b9de480b76b1f2774b83e66345bed65f *R/AffymetrixTsvFile.R
19119d0cfdae5ee12f7b078a5bc25b88 *R/AlleleSummation.R
e1b52cc0298380d1a8f4a175cbfe7c4e *R/AllelicCrosstalkCalibration.PLOT.R
2e3c59ae7ffd3e9138fe197b385c2aac *R/AllelicCrosstalkCalibration.R
1c91dccd5013bf3d659b82c9392d8485 *R/AllelicCrosstalkCalibration.getSetsOfProbes.R
a18f03a2134aca39169a191bfc2da067 *R/AromaCellCpgFile.AFFX.R
dd6c5343a0e54dd1076bc6a4ec798176 *R/AromaCellMatchScoreFile.AFFX.R
f075d494a8ab32693d60b405c0896344 *R/AromaCellMatchScoreFile.R
0204582d3e50513779302a596ac5d24c *R/AromaCellMatchScoreFile.importFromBpmap.R
42e9f6cee2c0c24bfed9cfa5db00bf2e *R/AromaCellPositionFile.AFFX.R
e6205a29f70b50a6eb0e99c632c35d00 *R/AromaCellSequenceFile.AFFX.R
0f445e7a2de2cb61e4218d0d927eee44 *R/AromaCellSequenceFile.importFromBpmap.R
b39c0b0756771af7c1c32e6bbac8dd70 *R/AromaChipTypeAnnotationFile.R
d59d8a6199e6b8469303fe8f4aec457a *R/AromaPipeline.R
697cbee9693526c970b81ec9de7f29e3 *R/AromaUfcFile.R
5528142cca73f7e6bcde221969ebe88c *R/AromaUflFile.AFFX.R
3afeae1ad1c21f3be2829fda191a653d *R/AromaUgpFile.AFFX.R
1d7fcaf120f60d752e7fc85675629166 *R/AromaUnitGcContentFile.AFFX.R
4b6bef7bfdc8e508d67a006ca2ba027f *R/AromaUnitTabularBinaryFile.AFFX.PLOT.R
9904dd336758511cabca9ede4c3e56f9 *R/AromaUnitTabularBinaryFile.AFFX.R
82e145656c0f5910019341f74131b69c *R/ArrayExplorer.R
d964ed7bb0f0a0ba7b978361e1a719be *R/AvgCnPlm.R
bfb01c72a718b90dda737ae2081ef33a *R/AvgPlm.R
2db2a0e0b972fc77abda390e3cea585e *R/AvgSnpPlm.R
cf80b9ffcb7b246c57537741dc13d4bb *R/BackgroundCorrection.R
bc767f4197cf1dceec194cb6056811f9 *R/BaseCountNormalization.R
8a1c88b779da4055a80da6aa50acb473 *R/BasePositionNormalization.R
dd8898688cee0d01b8ec41a267290476 *R/BasePositionNormalization.getFit.R
f89359ea86b92fa41d365d143ed3a4bb *R/ChipEffectFile.R
d16b4dbe009d5eb614b74d31e5b9493b *R/ChipEffectFile.TOFULL.R
8354315fd5473f89b90013897f343501 *R/ChipEffectFile.extractTheta.R
2be7311f5db756474804fa9ef943d7a2 *R/ChipEffectFile.fromDataFile.R
c865b3c51fb37d787a6b5b43f67a980b *R/ChipEffectFile.getUnitGroupCellMatrixMap.R
f04882d8e1a0c1b6613ac29f2cd8c913 *R/ChipEffectFile.xam.R
b291819e953b0adabc35d1fb4847234a *R/ChipEffectGroupMerge.R
5be336f9817c0de390e07a0a19a5502b *R/ChipEffectNnn.extractChromosomalDataFrame.R
d027b9de734a5b5f45a0c2ff5cf56750 *R/ChipEffectSet.PLOT.R
b3828736f09a5c44ad588dfcb487fcb7 *R/ChipEffectSet.R
2453b7aba45dbb65f6840cb2f15dbc42 *R/ChipEffectSet.STATS.R
223696f2a3644ec3aa0469e745a28612 *R/ChipEffectSet.TOFULL.R
fdf6d30908dc526d919d146c5e2db604 *R/ChipEffectSet.calculateBaseline.R
cfbb2bd7288454b77ea4167c5775e6b8 *R/ChipEffectSet.extractExpressionSet.R
61ac5af168ea27f2e71c51c38f30e70c *R/ChipEffectSet.extractTheta.R
1b4a98c3690d9edb4dd27514587045c3 *R/ChipEffectSet.getBaseline.R
3e35d1288f1dd23fcbba6a4cecb1a5e7 *R/ChipEffectSet.xam.R
45c95eb30f815da0add6f5c25bfe1f2d *R/ChipEffectSetTuple.R
e46c4b7eedf50fce80356c9e4903d499 *R/ChipEffectTransform.R
058de468d5c96289ba0040a837b5469e *R/ChromosomalModel.AFFX.R
a282fdfc67dcaf153523fac0e911a400 *R/ChromosomalModel.getPositionChipTypeUnit.R
4fed875c451c1394ee96f57bcaf4bc59 *R/ChromosomalModel.getXTheta.R
fc599889d7d5c70ac25df8ee52d6831e *R/CnChipEffectFile.R
b871fa6332428e3c8bf5a126ebe0e06a *R/CnChipEffectFile.exportAromaSignalBinaryFileList.R
0253e3d6a3969c221449ffb0ba9546a5 *R/CnChipEffectSet.R
4bc523c89ba611c92995d56778c05782 *R/CnChipEffectSet.importFromApt.R
3990813019093ccb6b1415beaf549024 *R/CnChipEffectSet.importFromDChip.R
dd1f3aa432496c87fadc6cc374e0ae4f *R/CnChipEffectSet.writeWig.R
885557e308583eab6b5790f8bfe215a7 *R/CnChipEffectSetTuple.R
715ae5520373360b3baf64c0a9d95c4c *R/CnPlm.R
5129350dd39de4b87d9d955cc3323584 *R/CnProbeAffinityFile.R
ba60ae74f8476df01ada5cb403bc599e *R/CnagCfhFile.R
cb6118e587eb0c223c888a803d7803e6 *R/CnagCfhSet.R
a2faaee83c703f8d6f704c09277229c0 *R/CopyNumberChromosomalModel.applyCCF.R
f4abcae38c717d35434d49b3b9b154ed *R/CopyNumberSegmentationModel.migrateTool.R
1231d59e7d8402287c541943eb10b3b7 *R/CrlmmModel.EXT.R
b16e385713841c8385f5e7b7212d9d38 *R/CrlmmModel.R
4d6f34f1f5505d906a7faac387a37bbf *R/CrlmmParametersFile.R
d8b5fa2c52f7d71e87dac5b09d8992fb *R/CrlmmParametersSet.R
8c54962900601fa4564660474b3974f3 *R/DChipCdfBinFile.R
a2bd9332769c3d60914e966bf2142f3b *R/DChipCdfBinFile.mapToUnitNamesFile.R
07cd9ffbb90b3471e7c5a36c91c0d674 *R/DChipDcpFile.R
1d4208e5a62281008e3584c9f601e4eb *R/DChipDcpSet.R
b43dd0be0980d3b3346b4a6bcf3413e3 *R/DChipDcpSet.extras.R
3ff8c9e87bd1d7b1bcc601892f8ad336 *R/DChipGenomeInformation.R
90a50740ece50c8aa786f7567f292785 *R/DChipQuantileNormalization.R
73a80f0f5c7e5911202c7b4ccf565446 *R/DChipSnpInformation.R
5e7b277cf683ace62b1d8aaa47769577 *R/ExonChipEffectFile.R
24cc6001725330dd06607b6a61dcabc1 *R/ExonChipEffectSet.R
92255be98fb194b53fa7f61ae01f0082 *R/ExonProbeAffinityFile.R
e1bec096d22066e895c4c878ed6749e9 *R/ExonRmaPlm.R
12ac3acc407e19064f251e74e8f34279 *R/ExonRmaPlm.calculateWeights.R
bf6ecc550c3619c1651e1601047acb9d *R/FirmaFile.R
a5ef3097e3a9eb96e14bc7c9bec9c259 *R/FirmaModel.R
88566625ba9e6864736d3f9ca44a1004 *R/FirmaSet.R
68d830f093f16a47637fe5061ae8ed9c *R/FragmentEquivalentClassNormalization.R
ab356b3e8d1fb3a9a38b663079f3a344 *R/FragmentLengthNormalization.R
0098fc46b4359ef25b1c1ea82a88c1e1 *R/GcContentNormalization.R
a93402fd96d8ec5971664458318a5c1a *R/GcContentNormalization2.R
7eebcd1ca32deb5ec0cadce5abc97e49 *R/GcContentNormalization2.plotCovariateEffects.R
f4576044c6beea2971e4b070b82adb8e *R/GcRmaBackgroundCorrection.R
eef9efe5b861e8dc23e559bb902146c7 *R/GenericReporter.R
6a3431d13e43f68d19ea703016175d14 *R/GenomeInformation.AFFX.R
7d38c115eccc3d134c263b90890ce599 *R/GenomeInformation.R
1362b6432c95cabaaf90da3496a31e3a *R/HetLogAddCnPlm.R
baba0451573065d544fd1813e93d6ddf *R/HetLogAddPlm.R
6b4c40c760a688738b390cf8b24b8ffb *R/HetLogAddSnpPlm.R
5d1c77a4e8e703bb662b0801e62c2b42 *R/LimmaBackgroundCorrection.R
d870d414f59b6269feb042613f1202d4 *R/LinearModelProbeSequenceNormalization.R
f2aa6f6544fc416bd18b716f62b4e77e *R/MatNormalization.R
eb14c2ae7b80b953e2b4201026d9278b *R/MatSmoothing.R
ab8305a6d637586411d3fe1300a8d2ca *R/MbeiCnPlm.R
03333fb6e2839534dc4a0b604b98a33f *R/MbeiPlm.R
98a9e5b2dd5639daa0c685bd62956101 *R/MbeiSnpPlm.R
d6b71e1fc42017ba782711b80b39eb76 *R/Model.R
a4098b7293b0576235b39316fe3253aa *R/MultiArrayUnitModel.R
06bdfacf4606480b7a1abbd35cb50e60 *R/NormExpBackgroundCorrection.R
a154c6f2f92b97a0462500a9a14c16da *R/OpticalBackgroundCorrection.R
9388086af14d2145806a908149b6fa41 *R/Package.XTRA.R
e99e58c5197528adaba12545fcab9fab *R/ParameterCelFile.R
09c8392e04efef1142d31f84cc8b98a2 *R/ParameterCelFile.extractNnn.R
232bcd61863467a90d19b179daa343e2 *R/ParameterCelSet.R
03c837d26e497acb0f9aae70e5b94ad8 *R/ProbeAffinityFile.R
e17249275cd130c8c3151d169891c176 *R/ProbeLevelModel.R
bde06981763b6fda8dfdded4ce39f773 *R/ProbeLevelModel.calculateResiduals.R
53f4b22e5c49bfb63227f97f65c83e3d *R/ProbeLevelModel.calculateWeights.R
37f0a7bc87f22dacb3781861d62625b9 *R/ProbeLevelModel.fit.R
f5d3a745926e64fe5914e9056a115d09 *R/ProbeLevelTransform.R
2d02fd693bf89a847beeecaac214994f *R/ProbeLevelTransform3.R
8d1951f9b492d596751cd437aac47338 *R/QualityAssessmentFile.R
5980413044ffc7f9a16a4179ec3fa55c *R/QualityAssessmentModel.R
cd4ad27696391d0cfc86c36240380680 *R/QualityAssessmentSet.R
79f8e220e31075c89f3f066e7f14ec63 *R/QuantileNormalization.R
0b46865a2c68399caf944c9f45a6bfe7 *R/QuantileNormalization.xtra.R
5f9d75ab92dda863e1ca14c506d3dd1f *R/ReseqCrosstalkCalibration.R
95416e0f5f89c0f8e57eac1fa2affcb8 *R/ResidualFile.R
b3c33de9049f3afd9be700a9846409cd *R/ResidualSet.R
07ea7fb52cc9f45acf244732d9f1cb4f *R/RmaBackgroundCorrection.R
ecf7f6b7c504251449179102670a4ddc *R/RmaCnPlm.R
84105ff7e57002e53ee4995498999225 *R/RmaPlm.R
122aa7007404368602d3918000c0f6e3 *R/RmaSnpPlm.R
335a951b45e5da232e3ff163754e8df3 *R/ScaleNormalization.R
d618d89555b8b0f6cea84728c7acb207 *R/ScaleNormalization3.R
a44d54d8c355a346fc861fd57155cc3b *R/SingleArrayUnitModel.R
7bd66e4ce257100ed5b05d1fc05193eb *R/SingleArrayUnitModel.fit.R
e5aac582b57d0b59dc2dda93ed3657f6 *R/SmoothMultiarrayModel.R
af3feeac775161919debcfdb39060bee *R/SmoothMultiarrayModel.fit.R
8415a030c231c59f069313f2ade43851 *R/SmoothRmaModel.R
271a88f24f0d8d421b99539576488f5d *R/SmoothSaModel.R
daa9a78f4baf6157af57474dc00bf102 *R/SnpChipEffectFile.R
d1771694d7674b5cdd1e53d661ff5fd1 *R/SnpChipEffectFile.exportTotalAndFracB.R
314602421853ba79caad94009f66cdee *R/SnpChipEffectFile.extractTotalAndFracB.R
464864cd959b63f701adf763361491d5 *R/SnpChipEffectGroupMerge.R
6b4cd8edc6f73ea5410d7950fd2b1c7a *R/SnpChipEffectNnn.extractCNT.R
3c33c0b92a71034bf1b680b3dbdf1c92 *R/SnpChipEffectNnn.writeCNT.R
e68588e451c49d8bb058668d5293ebdf *R/SnpChipEffectSet.R
f25155f57e0f982053f1c289d5290ce9 *R/SnpChipEffectSet.exportTotalAndFracB.R
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
0eb2d494a44f7d4af33ea690d262b1bf *R/SnpInformation.R
6ffa988e44e1411af39d304bb61f43d8 *R/SnpPlm.R
d213197b1c17a09b45abf7c13d59bd7f *R/SnpProbeAffinityFile.R
bf5f30204865b2ddd14564a9efb4ed49 *R/SnpQSet.extractTheta.R
da02985da5af1709f3b6c2cbe003eb53 *R/SpatialReporter.R
0872fabcb328e5b1f7860d9dba9843f7 *R/SpatialRowColumnNormalization.R
790a367320e8621a09e4b50c718078fc *R/Transform.R
108400b4d287573ff7c72dda144ea189 *R/TransformReport.R
3a3a7f246de9889998c23b89394a3467 *R/UflSnpInformation.R
120bc6cef692edc20658b0f0f7a711a6 *R/UgpGenomeInformation.R
03079a9c0f419d7e86cf43c5493bb495 *R/UnitModel.R
4446fc2fcb7bcc6aa8c08d8145fae80d *R/UnitModel.fitCnProbes.R
226c0faaf24e7c2661c9e2f590efff88 *R/UnitTypeScaleNormalization.R
fc2ea24267027cd2631f2dcf86a860bd *R/WeightsFile.R
c9f2e0f8e6580f18ca6f4d7e90e97c5b *R/WeightsSet.R
2b421c0f599c3c197b66d85f7398167a *R/bpmapCluster2Cdf.R
61efe30d6913889257b425664cac1adf *R/createExonByTranscriptCdf.R
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