a5451345c127926955db6b05f3acda8e *DESCRIPTION
faba816638d63f9394c1ca8eae50a8af *NAMESPACE
5ad3124dd6f77e009e56f548d053061d *NEWS
4bcbb5139128447d6309d89980703e1c *R/000.R
1df04dc13e5ad8dbc137a07bad5a1af1 *R/006.fixVarArgs.R
624fd58304f97d662bdc1a60a7774286 *R/009.setup.R
805a07eddfd4ae30baec1683fd3a1927 *R/021.dynamic_imports.R
63ed9fe6058b83af252076788d1a38e8 *R/999.AromaAffymetrix.R
34db1852eddfb6d44304fb3263e80290 *R/999.DEPRECATED.R
dcd82fd492e09e87908164709054a4d3 *R/999.NonDocumentedObjects.R
b28f6061a61060fd492c3718a752adf1 *R/999.package.R
cd99975062840994519e864c6f936fe5 *R/ASCRMAv2.R
5880bfe2fa17a291744707dc72bc354e *R/AbstractProbeSequenceNormalization.R
e89ec04fb5dec063e6efb6a4905ef1c1 *R/AdditiveCovariatesNormalization.R
fe21da79289e16df4521b85fe06453a0 *R/AffineCnPlm.R
7de1a4d28a1529f125d723d4f21971cb *R/AffinePlm.R
cadf7af3083fd78776c211a7b89be62b *R/AffineSnpPlm.R
f998a0b0bb0df8fb5af2a7b63643cd9b *R/AffyGenePDInfo.writeCdf.R
da3908f25666071f256f949c4b730a9e *R/AffymetrixAptSummaryFile.R
995bf893516471d125417da74f1f0974 *R/AffymetrixCdfFile.COUNTS.R
2f117c31d5e94af06c33ff3d66f1455c *R/AffymetrixCdfFile.MONOCELL.R
7c2749cf73b46af1f4535ff6d616662c *R/AffymetrixCdfFile.PLOT.R
38655712a18798286198867d81c27d0e *R/AffymetrixCdfFile.R
2088d692ca92d40fa3d0f9013ff5f61a *R/AffymetrixCdfFile.SNPs.R
f3e1e5e5ccdf726ac3ed553469d45aa3 *R/AffymetrixCdfFile.UNIQUE.R
f44ab508057aee488bc4da11b82f042d *R/AffymetrixCdfFile.computeAffinities.R
32d2074784b534b479298426fc3a2d0e *R/AffymetrixCdfFile.getAlleleCellPairs.R
b260ab1328553a6989a7140b05f72916 *R/AffymetrixCdfFile.getAlleleProbePairs.R
5c7aa93aa484f67b9fffcc4940e96aa3 *R/AffymetrixCdfFile.getAlleleProbePairs2.R
85afaf7ebcbcfb20faf669ecf740d287 *R/AffymetrixCdfFile.getAlleleProbePairs3.R
e684796d85dcaf95f0cb5c17024515ba *R/AffymetrixCdfFile.getCellQuartets.R
1d8e8c7b511d95234fec10b63a3ad90c *R/AffymetrixCdfFile.getProbeSequenceData.R
2d4bcac7c7e5fdd6aa5e4d0bebc4aea7 *R/AffymetrixCdfFile.getSubsetOfCellIndices.R
72492e7e8519ab2476f89aa1344ab027 *R/AffymetrixCdfFile.getSubsetOfUnits.R
8fd126f9cc0db05365150d26e8158af2 *R/AffymetrixCdfFile.getUnitGroupCellMap.R
e04c1d5ab2d2f34c87d11b4d47a69c69 *R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R
9fdeff4c13186194785941f2aaf9d009 *R/AffymetrixCdfFile.groupUnitsByDimension.R
cbaff645d5566ca5b3792da271a4b66c *R/AffymetrixCdfFile.readDataFrame.R
1c22aa834e192bc2621eb5d7bc8b05ff *R/AffymetrixCdfFile.writeCdfByExcludingCells.R
d41d8cd98f00b204e9800998ecf8427e *R/AffymetrixCelFile.BG.R
bc2c2aacef6309e06b42b0783c45358e *R/AffymetrixCelFile.PLOT.R
7d729e432446ce31c858217a88389b98 *R/AffymetrixCelFile.R
68f82fa46176c0c114993e8c2a0d83b4 *R/AffymetrixCelFile.allocateFromCdf.R
75cdbabcd26db75c565229f38d8ae2a1 *R/AffymetrixCelFile.createFrom.R
30b469cc2302916dcf27c6f8f90779ed *R/AffymetrixCelFile.extractMatrix.R
79815552c52cab5312673dee7a6212ed *R/AffymetrixCelFile.fitQuantileNormFcn.R
01fbcd961e47daf74e9e3a37de827445 *R/AffymetrixCelFile.normalizeAffine.R
967f031ace93d47987af4d65f19dd687 *R/AffymetrixCelFile.normalizeQuantile.R
c757037e503c64ea49c58990a7dd7896 *R/AffymetrixCelSet.BG.R
ca2de49cb95c433858dec3d81eeb6ae6 *R/AffymetrixCelSet.NORM.R
e40e9c1078408149f19de6a6a949a81c *R/AffymetrixCelSet.PLOT.R
76bb4b39c8152d453eb4ad4a16b4c106 *R/AffymetrixCelSet.R
9a7ece35d040300fb341153e0714113a *R/AffymetrixCelSet.convertToUnique.R
4b27d30099f8723c911ea0ca2fc70f85 *R/AffymetrixCelSet.extractAffyBatch.R
e6f095a317046dcb1b98fda6015d20f0 *R/AffymetrixCelSet.extractFeatureSet.R
b9db0e6a10d640b246c9d1174c7d7a79 *R/AffymetrixCelSet.extractMatrix.R
f34db3f1fc9e446fafa7581227c3870b *R/AffymetrixCelSet.getAverageFile.R
356ac091e3351e6d49bb94319c9cef52 *R/AffymetrixCelSet.importFromDChip.R
f3eaa5031cfb7833707cd4266403d693 *R/AffymetrixCelSet.justSNPRMA.R
557a0adb9c4250be3ada694745ac1fe8 *R/AffymetrixCelSet.writeSgr.R
e50b1f49ef81ae45765b7d6eeef9a308 *R/AffymetrixCelSetReporter.R
539eea912abffbc38120c0349a65a7eb *R/AffymetrixCelSetTuple.R
ae311eb872a0b7db4e96538337d2b745 *R/AffymetrixCnChpFile.R
f4b4578e1936d605fc084432c4dbe1e0 *R/AffymetrixCnChpSet.R
9e7751f2dc0c96525b6901e774ac1e94 *R/AffymetrixCnChpSet.extras.R
f501392343a5d8da7fa95b253e96dcb6 *R/AffymetrixCsvFile.R
abe28d4c0ab20d3692d534c06bb33388 *R/AffymetrixCsvGenomeInformation.R
d39ee32a4209d7f0cb21381a8d41ec60 *R/AffymetrixFile.R
34f283f5bb32a2c35ffe0bd25d8c56de *R/AffymetrixFileSet.R
4aa325fbf7fec4605ffa12567c735419 *R/AffymetrixFileSet.getIdentifier.R
2f7695fc6ae391118fbcb7cff4beaec6 *R/AffymetrixFileSetReporter.R
9e765b7bf64c1e47fdbbf066fa247e77 *R/AffymetrixNetAffxCsvFile.R
28bf78206a85d8aa9c073a17f0eb72a8 *R/AffymetrixNetAffxCsvFile.XTRS.R
4c34d87a17274ff36de2bde4d6925bcd *R/AffymetrixPgfFile.R
a600fa011165335d6d6d523ae6c3e3e6 *R/AffymetrixPlatform.R
a5728eecd4163324dbb952bf351df452 *R/AffymetrixProbeTabFile.R
65bd267c6cba1d7407ff243a15107f32 *R/AffymetrixTabularFile.R
65b67343047385c80c4e2c4affcdfa52 *R/AffymetrixTsvFile.R
f7c6a4903406f85c692b90178cc05cd5 *R/AlleleSummation.R
83e8a6a6a4d7b6e4fcd045a168962f6f *R/AllelicCrosstalkCalibration.PLOT.R
12cf9b67d1b6a2508a07618bc4c105be *R/AllelicCrosstalkCalibration.R
90d607990e62156ebdcd492201c21264 *R/AllelicCrosstalkCalibration.getSetsOfProbes.R
5f5b14970c430e305502e4ff584d9744 *R/AromaCellCpgFile.AFFX.R
ac03cc2a16b3f617c98b6feaeeab8d7f *R/AromaCellMatchScoreFile.AFFX.R
544f5ee5a65298b630f81ce79360faf2 *R/AromaCellMatchScoreFile.R
d15b9f8ebd7d15b16875de15fb8c0316 *R/AromaCellMatchScoreFile.importFromBpmap.R
b342ad91c3f0451ea16804bd12bab942 *R/AromaCellPositionFile.AFFX.R
c2667a51ba32985fae5dc8caca6e1d86 *R/AromaCellSequenceFile.AFFX.R
ebed0ff84250f57224fd7def783d5a98 *R/AromaCellSequenceFile.importFromBpmap.R
d90f8a04c578b572648944f3a2ad7715 *R/AromaChipTypeAnnotationFile.R
6a766934c0899decd0cc21075e94a561 *R/AromaPipeline.R
904000f217fd6dc624ac89b53ebae235 *R/AromaUfcFile.R
a6dadac84938e4d858e9f19a55424f33 *R/AromaUflFile.AFFX.R
51511a5db9a1ef2e827e3507a4e10b5a *R/AromaUgpFile.AFFX.R
3b8bf4d3c73d3025f7bab2cf4ca7257f *R/AromaUnitGcContentFile.AFFX.R
1f8db19cdb90805439b3ddf827eb6c96 *R/AromaUnitTabularBinaryFile.AFFX.PLOT.R
3a44120edea5f7732c3a237917cb81a4 *R/AromaUnitTabularBinaryFile.AFFX.R
1bd3539d3187eab578d8a7d44e412578 *R/ArrayExplorer.R
2afa51fc21c0f4b14b52111585b9de2c *R/AvgCnPlm.R
ee189b9b0e523973765dc2213d68d1f3 *R/AvgPlm.R
53adaf8514033c7ea63d2fb5e6ab511d *R/AvgSnpPlm.R
d3dc81c560f6ba067fb4658ed9466979 *R/BackgroundCorrection.R
62b4230c55c192c389a8e7ce633818b8 *R/BaseCountNormalization.R
6f1e03870b880b0cfb2837c0958e339c *R/BasePositionNormalization.R
bdae86f3d3304685715aaed155b1ccad *R/BasePositionNormalization.getFit.R
adec8d4eec1519a28ea569818b4abfec *R/ChipEffectFile.R
62cf790d84e513ec09fafb573a794f48 *R/ChipEffectFile.TOFULL.R
a23ef50e8e69bf3d35bbe25632b66c60 *R/ChipEffectFile.extractTheta.R
9560b03fe431ac123dd101db9a77975d *R/ChipEffectFile.fromDataFile.R
cde13e4b7e95d319be69584f5c60ee24 *R/ChipEffectFile.getUnitGroupCellMatrixMap.R
943e6b2b1548993005d21f9026399ca3 *R/ChipEffectFile.xam.R
d38f77a5b9869d537e103ebd2c4876e9 *R/ChipEffectGroupMerge.R
6ced08815cd7da9aeca51aa5e2b236e6 *R/ChipEffectNnn.extractChromosomalDataFrame.R
158a0332139367665996cfd6e9b5cb44 *R/ChipEffectSet.PLOT.R
88f49c3b8a03ed4d7c497198fc4600f4 *R/ChipEffectSet.R
df1f93d9d1c6ab6ed516a91fbcd66793 *R/ChipEffectSet.STATS.R
5148b2789f801800064b370d12b3d02f *R/ChipEffectSet.TOFULL.R
a95cb2984b9295dac148f2c1a5adb1d7 *R/ChipEffectSet.calculateBaseline.R
0e9b8ba018b3a70c20a47827c1e4aaab *R/ChipEffectSet.extractExpressionSet.R
edda411b17957d8ae2bd1a69eae0fbda *R/ChipEffectSet.extractTheta.R
e797b8d60cd98a06e9fde136ddbd407e *R/ChipEffectSet.getBaseline.R
0bf6f7c1b57c708d89140e94a45c53cb *R/ChipEffectSet.xam.R
e7173920d59ffd14c6661888a20e01e6 *R/ChipEffectSetTuple.R
c13cad9ac8378a6ceba6705719d66c09 *R/ChipEffectTransform.R
5ed8a3adbd7ab6bb4b37d3788e3dbb2c *R/ChromosomalModel.AFFX.R
959fc2f40bb55e82cb282f0d77f6a992 *R/ChromosomalModel.getPositionChipTypeUnit.R
7384f5324403bd93a0a0aad5d1e2cc27 *R/ChromosomalModel.getXTheta.R
0b64418053dd2bbbc0272ffdb8bac514 *R/CnChipEffectFile.R
a653efb46ecd18669abb901e912d91f6 *R/CnChipEffectFile.exportAromaSignalBinaryFileList.R
49041a3c3f952ca2b0c359c8a38ea7f3 *R/CnChipEffectSet.R
99c555ad6b679b91026c7ba8c0d0427a *R/CnChipEffectSet.importFromApt.R
b86d0182bc05eb91b0c24df475a289ce *R/CnChipEffectSet.importFromDChip.R
3101f79aac60b77407e2ae36883b9d57 *R/CnChipEffectSet.writeWig.R
4e11aa2014b57789e7bb6a4d8d3238fc *R/CnChipEffectSetTuple.R
ab8c82041137149bd4a349e5a6696d93 *R/CnPlm.R
605f0135b401f56df47a33b1f1b89008 *R/CnProbeAffinityFile.R
018f1e6ea174fec04af1375d4dc9c857 *R/CnagCfhFile.R
b04f45b16cb0474ef1e13ac80a0c0084 *R/CnagCfhSet.R
879ae89639db3ef33417eb32dd8eedc3 *R/CopyNumberChromosomalModel.applyCCF.R
b55b562041f36ba80ae669c359fd2635 *R/CopyNumberSegmentationModel.migrateTool.R
9fde3cd22cd7aa094806e9d9ecdcdf97 *R/CrlmmModel.EXT.R
1128dc56b42bfc42c85f1549cb4d2c4a *R/CrlmmModel.R
a80df6fe30efa7fa24bc48f1d89e67eb *R/CrlmmParametersFile.R
effd615a8dfa17d9693ba390493b5a31 *R/CrlmmParametersSet.R
e1efd3f479d0c0953844499d7088a2bc *R/DChipCdfBinFile.R
b114a829906953f349b91a133e3498fd *R/DChipCdfBinFile.mapToUnitNamesFile.R
97ef2624bb2a2c6581ee1f1959825201 *R/DChipDcpFile.R
6111a7cdb1573ee0cd0720150064e1d1 *R/DChipDcpSet.R
d29872a1795e90e7bdc56c0f6f0a92f4 *R/DChipDcpSet.extras.R
c90513d6cb1254e2d2d2966cc2356adb *R/DChipGenomeInformation.R
bea37a97078736c59eb19fba5c646b78 *R/DChipQuantileNormalization.R
8d30a18d2bc3005fa6721a0b10bfec3a *R/DChipSnpInformation.R
f8c4c84f2c869539148c6a33e61e3c9c *R/ExonChipEffectFile.R
cb86633bd0ea6bdb3b90a11c9db1c8f5 *R/ExonChipEffectSet.R
4492c4178cbe7116011ee1f89875f896 *R/ExonProbeAffinityFile.R
8463e92057cb75493b6052129eb3228b *R/ExonRmaPlm.R
c2629f648de6ea0bcf608905a55e7e4c *R/ExonRmaPlm.calculateWeights.R
585406092dd2302c7a811d0be243d53b *R/FirmaFile.R
f4bb6d4df073c2a12c6bffd436760943 *R/FirmaModel.R
06ed7666e99ac42848ff290e4dce1c49 *R/FirmaSet.R
6d43ec9ccee4d7b3e3f67885789919ef *R/FragmentEquivalentClassNormalization.R
f193fb181c8a9ed0196d115790089481 *R/FragmentLengthNormalization.R
fd22c063c06d6f438d42eddc3e0c3ea1 *R/GcContentNormalization.R
db989ad13189ef04cf2aec3fa1abf5cc *R/GcContentNormalization2.R
d26563141c82f24c7ef39210ec298e83 *R/GcContentNormalization2.plotCovariateEffects.R
dc0e8fa5da814c5699c48b5f2d7f7fcb *R/GcRmaBackgroundCorrection.R
e1dfbf8a971e057f8fe8b4f4d06dbc34 *R/GenericReporter.R
2dc659df08be48dcd060ce0a1a260824 *R/GenomeInformation.AFFX.R
f006fce55458a3095990ff3e63c43c7e *R/GenomeInformation.R
f623fb68d2662b79308b856439b33a87 *R/HetLogAddCnPlm.R
541c905ca30f6804d4ef7b9c9b9023f5 *R/HetLogAddPlm.R
fca47b60345502984d788761d89d8719 *R/HetLogAddSnpPlm.R
b79ec361bd3061a8608b53fcd1981e7b *R/LimmaBackgroundCorrection.R
3f3ff8cae1d1b61e24ebf1be4d09e596 *R/LinearModelProbeSequenceNormalization.R
9f9fe1dde2d51a798c155f0757bfeb38 *R/MatNormalization.R
808560bc9440ca11ede975e897d983c2 *R/MatSmoothing.R
d2290c579d1c5e3cefb3856a011cdfe2 *R/MbeiCnPlm.R
7b4ab4350fd1ff4946d3241e0a89a82b *R/MbeiPlm.R
0a524d52f05ad9a942dc2e82ef768093 *R/MbeiSnpPlm.R
91d93c9e4ce268828cd887aee6bf0996 *R/Model.R
eeeb2055dda83387565f74db1b11c655 *R/MultiArrayUnitModel.R
84fff9cc6e2bb1fe08a4fea74842b9c2 *R/NormExpBackgroundCorrection.R
ee5a504d6e64220b9b32818b366c36be *R/OpticalBackgroundCorrection.R
d562d34864edf5bfc6fa85cb7a928ee0 *R/Package.XTRA.R
ef01eef2880483648ffd17a3840c1250 *R/ParameterCelFile.R
4644efb0fb59bf1c870c6ba8020e0282 *R/ParameterCelFile.extractNnn.R
3f6697b564ceef2d847a527f38fea7b3 *R/ParameterCelSet.R
28a8f22e374a32483de9955975fe1074 *R/ProbeAffinityFile.R
4d16635769bd4c4c3b638d66e7769e1f *R/ProbeLevelModel.R
26f37028f4a1084e8bf7b4b25282748b *R/ProbeLevelModel.calculateResiduals.R
56d5ee3bb52a8da48f0f68000e7d6117 *R/ProbeLevelModel.calculateWeights.R
0587d575c9d5b0b7af66138dd5bb23e1 *R/ProbeLevelModel.fit.R
768245b84d744f0faafd77ec3bc70ec8 *R/ProbeLevelTransform.R
6ef0d1bb71c01ec74a4cd20e9681f40f *R/ProbeLevelTransform3.R
0a4f14f9347d2b03d7a6214864b9f8c8 *R/QualityAssessmentFile.R
224cc519591349f22461d443364d5f8b *R/QualityAssessmentModel.R
9ad089ecce42f2da020413b53c78bfc0 *R/QualityAssessmentSet.R
ec0bbef8b152f6b54707901e2aab8a84 *R/QuantileNormalization.R
f53ce02d8822f35717b682ec2dfd51a9 *R/QuantileNormalization.xtra.R
1ae036159ba7ce0bac652c6834729033 *R/ReseqCrosstalkCalibration.R
4159de4ab7b6d2a8f64d7bf643a41629 *R/ResidualFile.R
5890c62ec2cf221ddd705ae9f9842622 *R/ResidualSet.R
6ff83ba5ad462a9b313ce129126a10d4 *R/RmaBackgroundCorrection.R
2afa17e51f48c77713ff04fcaf9babb0 *R/RmaCnPlm.R
6542c299afb6bd8de12c3efd21e58f0c *R/RmaPlm.R
c300dc6c9f336fd7efb825ad875866da *R/RmaSnpPlm.R
baae1247a1f38ba7a50fe2d2625dc1c4 *R/ScaleNormalization.R
c9dc162de4cc8842021a2553281060bf *R/ScaleNormalization3.R
44544e46516f3b1312fdec91cd033e07 *R/SingleArrayUnitModel.R
5f46dff0909a56d0dd33e7536a0dd80e *R/SingleArrayUnitModel.fit.R
9553228b154fa3e7071eaf3b60e24f19 *R/SmoothMultiarrayModel.R
b95759a8b47427ef31f7c934fd49fb2a *R/SmoothMultiarrayModel.fit.R
bc1a59e484a1724d41119e7e0ad8f4b8 *R/SmoothRmaModel.R
c412796013c65af4739eb778d8b008fe *R/SmoothSaModel.R
edc04085e2443300f59c5b80eb378618 *R/SnpChipEffectFile.R
f0015de0975a30f15670de77b9063d7b *R/SnpChipEffectFile.exportTotalAndFracB.R
4e6ca7156366affd86406cdb00938b1e *R/SnpChipEffectFile.extractTotalAndFracB.R
cbb0aa381ff631ad23b5c53be4ca942f *R/SnpChipEffectGroupMerge.R
8095247eb2c666f7443b9bfd30e337a6 *R/SnpChipEffectNnn.extractCNT.R
bec9cb022189b1f9d1836e4d151b2243 *R/SnpChipEffectNnn.writeCNT.R
0695e4affffcf40d5647902fe396a776 *R/SnpChipEffectSet.R
87320102fe64f066c648b01adaef117f *R/SnpChipEffectSet.exportTotalAndFracB.R
25e976ee273492610d324e87487891b9 *R/SnpChipEffectSet.extractAlleleSet.R
ae94c1546ebd4cd1c61d1653fc8514aa *R/SnpChipEffectSet.extractSnpCnvQSet.R
1afcec4b3cee3ac66e9e471a9b5dd553 *R/SnpChipEffectSet.extractSnpQSet.R
cf16a32fda1d44c0db24ad04e8bd8699 *R/SnpChipEffectSet.extractTotalAndFreqB.R
a3c2875c17831e28e3272660e57e10ed *R/SnpCnvQSet.extractTheta.R
9413490601e1a06caefd444698c54d4e *R/SnpInformation.R
fbba483081b42a51e24eeeab603a0892 *R/SnpPlm.R
7ea8dfdb08dbc17c8d116b21baa2fd68 *R/SnpProbeAffinityFile.R
b26273b1236fdee92b80720410ad7581 *R/SnpQSet.extractTheta.R
0806f2f018ab06273172cf8aecd45673 *R/SpatialReporter.R
936303eb7c934bf98046510ad4f9931d *R/SpatialRowColumnNormalization.R
6eeed759652df29cbc828c23bc059600 *R/Transform.R
f4fb09205462dccbc80137ba69b3e526 *R/TransformReport.R
55ad5732f3066495b6c4e523d6e0f180 *R/UflSnpInformation.R
137d9113aaa77a332f7902995632450a *R/UgpGenomeInformation.R
6461deab7bc87ff61f3395d00613a83c *R/UnitModel.R
8395cb5177856f52098e1b4aef3d6aa0 *R/UnitModel.fitCnProbes.R
d2878fb2f3dfb07215e2f39e81b05f09 *R/UnitTypeScaleNormalization.R
2ba72859b4fbc72076c2948d74cb1a53 *R/WeightsFile.R
6d51f2d5dfba931e936acb90ccebcc8f *R/WeightsSet.R
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