6404fa1bee9ba1ba788ff78f7e5ed909 *DESCRIPTION
85a6c457a89b54e08f57a95d9a6b33fc *NAMESPACE
5838458a52d3c0edfcf8e4a669260be6 *NEWS
4bcbb5139128447d6309d89980703e1c *R/000.R
b6d1bef5586736c914f5336ef1f08e1a *R/006.fixVarArgs.R
ee7af24de9e03e26b18ae820ff0c196b *R/009.setup.R
53391180ce8a3d3634efadbd34975858 *R/021.dynamic_imports.R
2fa01bc3e3a8559f3f929097f350ffd2 *R/999.AromaAffymetrix.R
7c4f3615fdddb22863d962fd33b31e5e *R/999.DEPRECATED.R
ae5c7a6c9cd6ac16c5192b8acb930e5d *R/999.NonDocumentedObjects.R
0225dc84810194f393299d924596406a *R/999.package.R
c499bbe1c8e3e38fd1b3f1cd90b1e50c *R/ASCRMAv2.R
267f6669ad303f5866fc61ce65a63a07 *R/AbstractProbeSequenceNormalization.R
39122d759b2d3f0d6bddc24d887922fc *R/AdditiveCovariatesNormalization.R
662fecb270ac1a63af7dca52e7a963c2 *R/AffineCnPlm.R
899270cf2a2dc107e94d9773d6b25317 *R/AffinePlm.R
302bb9c345b292b058453e84a51afe21 *R/AffineSnpPlm.R
becd7b25f29cf83a7bab4337516b8eaf *R/AffyGenePDInfo.writeCdf.R
9d3b3364031b8a044ccf1fe07d3d1142 *R/AffymetrixAptSummaryFile.R
1eb87c9122c230b3464857ef9be3a21a *R/AffymetrixCdfFile.COUNTS.R
35ddcf7d5d0c336905ce4278cc8f8c03 *R/AffymetrixCdfFile.MONOCELL.R
eb0d862f92be07f3a63df33217a3af6a *R/AffymetrixCdfFile.PLOT.R
7ed85be9bfde77e5fc71f21c22f8e029 *R/AffymetrixCdfFile.R
b1b2462faad4542b6091ca92310e1abc *R/AffymetrixCdfFile.SNPs.R
57e1cd7a94eb7ed746fc0609fd5e88d4 *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
405f1c7144072ee626f9f8f57f5853be *R/AffymetrixCdfFile.getSubsetOfCellIndices.R
6ff15d927e6e5f9c0c32337cb07f8aec *R/AffymetrixCdfFile.getSubsetOfUnits.R
5f69c0313c1a8564790b7343f7324346 *R/AffymetrixCdfFile.getUnitGroupCellMap.R
dcbffca4285dc229c34ad6fc3b36bcb3 *R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R
5bf4fd73e65a98804043aeb7534a449e *R/AffymetrixCdfFile.groupUnitsByDimension.R
e5d2cc9bfb57e55b2e162bb7e2b3cfd1 *R/AffymetrixCdfFile.readDataFrame.R
13461a60807eb8d9120299ae6fde5680 *R/AffymetrixCdfFile.writeCdfByExcludingCells.R
d8a6ec4019c1b02be11b5fee1b00ca9e *R/AffymetrixCelFile.BG.R
7fd82f4c3c6aab2d6209fa4059c5a165 *R/AffymetrixCelFile.PLOT.R
f13452b0e74ac615b290e96880ae12b3 *R/AffymetrixCelFile.R
7b485819bb9b7ca0e66dcd3ea98bb4c3 *R/AffymetrixCelFile.allocateFromCdf.R
8dc322e91e7a8cdb212c3305981f9758 *R/AffymetrixCelFile.createFrom.R
57a6c85aa4323648eb42209a7cadcd40 *R/AffymetrixCelFile.extractMatrix.R
1d2a893fd8257bc2299f41adccdefe79 *R/AffymetrixCelFile.fitQuantileNormFcn.R
8235060687f5f6fc09c146c76e924762 *R/AffymetrixCelFile.normalizeAffine.R
1e6167a09fdc9307a44ac0e4a0656443 *R/AffymetrixCelFile.normalizeQuantile.R
e170cce0ef8f34b7c092759fddc28177 *R/AffymetrixCelSet.BG.R
d7acbad8e179f41ac6fa5ae6ad3ea681 *R/AffymetrixCelSet.NORM.R
836190e5c9852b10494f449c1f9ae199 *R/AffymetrixCelSet.PLOT.R
cc12c5e7c91a3ba63e28b62493c07316 *R/AffymetrixCelSet.R
4851c79602af11f89b729d70c279cc4a *R/AffymetrixCelSet.convertToUnique.R
2a5b592ebd4cc236a0fc5d77a6c4f704 *R/AffymetrixCelSet.extractAffyBatch.R
008d86ddfd3f64ce1006c63f43941ce9 *R/AffymetrixCelSet.extractFeatureSet.R
ddc472cc37e9494e6ae8dfce72c96166 *R/AffymetrixCelSet.extractMatrix.R
53a14e671abc0b6e920ca97a05a3bff6 *R/AffymetrixCelSet.getAverageFile.R
d2513610b00e6563b37698fe70be2bd8 *R/AffymetrixCelSet.importFromDChip.R
87b7abc2139a8e3bbef7051fcc23e136 *R/AffymetrixCelSet.justSNPRMA.R
bd57c24f7470da248dec0e040e429dd3 *R/AffymetrixCelSet.writeSgr.R
efbcac9bcbcafc8045c39cb2c7f891a0 *R/AffymetrixCelSetReporter.R
ad71e397fe6314b88c5a691f904d3be8 *R/AffymetrixCelSetTuple.R
ad58aa07adacdc7014a29e198f79543e *R/AffymetrixCnChpFile.R
2994e548034413c83167fbe3a96ace3f *R/AffymetrixCnChpSet.R
cca2adfff27f21ec3ee0734ea9a65919 *R/AffymetrixCnChpSet.extras.R
241911b539f350a3466905f59cdad8b8 *R/AffymetrixCsvFile.R
d2362c5a509a9c5da557b087379fa545 *R/AffymetrixCsvGenomeInformation.R
76b78dc4df66bf782e3b60d28dd0dcc1 *R/AffymetrixFile.R
dad81031df1f7cc3495c61900e939437 *R/AffymetrixFileSet.R
9daa660e9ab06235c2b92b4fe64f8883 *R/AffymetrixFileSet.getIdentifier.R
22a40b6b1c27bbaf459b7a043a1918b0 *R/AffymetrixFileSetReporter.R
6f1d73f887854c9d761c8e20f5db1805 *R/AffymetrixNetAffxCsvFile.R
05d3fd51717d57099b7727e6e182ca62 *R/AffymetrixNetAffxCsvFile.XTRS.R
104bc40c8e030dcb9d08aefb86fc37c2 *R/AffymetrixPgfFile.R
ded561fb8f66c729df252452bea645dd *R/AffymetrixPlatform.R
e0c23389df6159ae18b7bf958bcc7396 *R/AffymetrixProbeTabFile.R
17492538f44aa5596275cfdc1738f440 *R/AffymetrixTabularFile.R
edba22732e8dd2cc44b2fec289173d96 *R/AffymetrixTsvFile.R
dbb895c4c702ac60b86196a45af08eac *R/AlleleSummation.R
ead56362ebbe0966957b4169878bf53f *R/AllelicCrosstalkCalibration.PLOT.R
e6170f1c78f374595587cbbc37289b4c *R/AllelicCrosstalkCalibration.R
0a66118acf349aea6f205943b488b49e *R/AllelicCrosstalkCalibration.getSetsOfProbes.R
a18f03a2134aca39169a191bfc2da067 *R/AromaCellCpgFile.AFFX.R
dd6c5343a0e54dd1076bc6a4ec798176 *R/AromaCellMatchScoreFile.AFFX.R
22833ce19e8d15afff48ca88b5372062 *R/AromaCellMatchScoreFile.R
96bc147809648e700f322faf93350365 *R/AromaCellMatchScoreFile.importFromBpmap.R
42e9f6cee2c0c24bfed9cfa5db00bf2e *R/AromaCellPositionFile.AFFX.R
79a7c675c2cef6de74065939cc1fac23 *R/AromaCellSequenceFile.AFFX.R
5217683b8d212344c980711e7a10df45 *R/AromaCellSequenceFile.importFromBpmap.R
b468139c69d3dbd432f1da35ab3876c9 *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
094d863be46737cd5d27001c7011236e *R/ArrayExplorer.R
d964ed7bb0f0a0ba7b978361e1a719be *R/AvgCnPlm.R
14e49fde2416040a39646790de398818 *R/AvgPlm.R
2db2a0e0b972fc77abda390e3cea585e *R/AvgSnpPlm.R
cf80b9ffcb7b246c57537741dc13d4bb *R/BackgroundCorrection.R
8724235090dbe56880e7173d4191f85a *R/BaseCountNormalization.R
a806a49b4a8ccad9d5e489e9dc21a103 *R/BasePositionNormalization.R
ad22c0e9d6630defae357e03b6c46b95 *R/BasePositionNormalization.getFit.R
d413aa10022b185b297e384123e8e622 *R/ChipEffectFile.R
47b57272ade8297b59627ea71effbb17 *R/ChipEffectFile.TOFULL.R
8354315fd5473f89b90013897f343501 *R/ChipEffectFile.extractTheta.R
ea3568dbda6638f6c11436f10ed1fe0c *R/ChipEffectFile.fromDataFile.R
02a9ddffb4d6208601e1782c5c89a466 *R/ChipEffectFile.getUnitGroupCellMatrixMap.R
6a96a795391b4fd5546ecd721d50c23f *R/ChipEffectFile.xam.R
042bebd527cca9a787668770a58c4f29 *R/ChipEffectGroupMerge.R
0c5330f0e9f7131c74bd10689ea097e5 *R/ChipEffectNnn.extractChromosomalDataFrame.R
d027b9de734a5b5f45a0c2ff5cf56750 *R/ChipEffectSet.PLOT.R
b6741c787a5df3e52572b2ff1c2010b2 *R/ChipEffectSet.R
dd4ad040b79cdad4c8af80aae65aad11 *R/ChipEffectSet.STATS.R
63a5a603e07200c7f37cce98f6ac70fa *R/ChipEffectSet.TOFULL.R
7ad0db18b8fc22f334d5953fe93b7718 *R/ChipEffectSet.calculateBaseline.R
6cefc2a12fb776e8f72945638a3c783c *R/ChipEffectSet.extractExpressionSet.R
27bc89f3898e27032f1164e8f91aca44 *R/ChipEffectSet.extractTheta.R
a5646fb6e1ef68c381be9c4209447db9 *R/ChipEffectSet.getBaseline.R
2b0ce51a734bd62d4b83cd1dd13a794e *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
3010abcbb7f1900aff73ed3622cd3787 *R/CnChipEffectFile.R
b871fa6332428e3c8bf5a126ebe0e06a *R/CnChipEffectFile.exportAromaSignalBinaryFileList.R
2ce5364fcad1f05084a2079cab8edfef *R/CnChipEffectSet.R
4fb10505ef3227b5d7f176a638bcdcf9 *R/CnChipEffectSet.importFromApt.R
c39f6b80dabc795a18eae94c0ae84588 *R/CnChipEffectSet.importFromDChip.R
fe5a7a6dfecd586a77b071a5b7ac60df *R/CnChipEffectSet.writeWig.R
885557e308583eab6b5790f8bfe215a7 *R/CnChipEffectSetTuple.R
24d84efc48dafb3fec020afa77832294 *R/CnPlm.R
e29643fc3e318f20886b4ebe2bb04958 *R/CnProbeAffinityFile.R
6ee31219f6c01cb6d614e4e887ec7de4 *R/CnagCfhFile.R
c6bcdff96d37544402c7120e852aead0 *R/CnagCfhSet.R
9c0eb4fbcf7f7b5a319607d5d606c427 *R/CopyNumberChromosomalModel.applyCCF.R
f4abcae38c717d35434d49b3b9b154ed *R/CopyNumberSegmentationModel.migrateTool.R
2326cb79143b2c129acfe8f164eb68fb *R/CrlmmModel.EXT.R
cfead916596b46853955079909b4f238 *R/CrlmmModel.R
4d6f34f1f5505d906a7faac387a37bbf *R/CrlmmParametersFile.R
7c4dbc341545a3fe08bb339b8f0c8a2a *R/CrlmmParametersSet.R
82500c03205725be8b946db0d5494eb7 *R/DChipCdfBinFile.R
9449523da7357c4438a9fdc5235397a8 *R/DChipCdfBinFile.mapToUnitNamesFile.R
6141cf179d0a31f97cafa94785d3b7f3 *R/DChipDcpFile.R
e37abe947845555dd34893dc8df3851f *R/DChipDcpSet.R
8c5b2679723549cf9014697f7a8b702a *R/DChipDcpSet.extras.R
e7a3143dd56d5bcfba04af41ec046014 *R/DChipGenomeInformation.R
7c9ca6804e5f3f13cfe78817690791cf *R/DChipQuantileNormalization.R
73a80f0f5c7e5911202c7b4ccf565446 *R/DChipSnpInformation.R
3e81635a31779faacde1bdd3211f33fb *R/ExonChipEffectFile.R
8da6db9f361cfeb767b3cc8bf8278f34 *R/ExonChipEffectSet.R
266b92452ab3531f18a057e8186b35bf *R/ExonProbeAffinityFile.R
9e1c16cc1fc6610e4035477a3f509b1f *R/ExonRmaPlm.R
7de369ac6428193eac47046d7ada46fb *R/ExonRmaPlm.calculateWeights.R
86c961524dbdfdb6eafc54bac2eb47d3 *R/FirmaFile.R
dcd676506d900e0f5f3bbec9c3b08b51 *R/FirmaModel.R
af23a680e54e1b20a19eb21888843244 *R/FirmaSet.R
f032cc47339a1074d2e82491d91905cf *R/FragmentEquivalentClassNormalization.R
a8098fabeeba6ba6c33350a5da98d093 *R/FragmentLengthNormalization.R
78e9ed88c337989f48de123c32b5d072 *R/GcContentNormalization.R
a93402fd96d8ec5971664458318a5c1a *R/GcContentNormalization2.R
01579a9c9d212196f99b46b1145ad623 *R/GcContentNormalization2.plotCovariateEffects.R
f4576044c6beea2971e4b070b82adb8e *R/GcRmaBackgroundCorrection.R
251fe86b692e1301dd8a8a9b448ed873 *R/GenericReporter.R
4bae2dc2451069ed61e28a3f53304bcb *R/GenomeInformation.AFFX.R
394380ee8b62d1f1115a9a45e27b8d9b *R/GenomeInformation.R
1362b6432c95cabaaf90da3496a31e3a *R/HetLogAddCnPlm.R
77ef80f6c965d1469629e439b0dba6cd *R/HetLogAddPlm.R
6b4c40c760a688738b390cf8b24b8ffb *R/HetLogAddSnpPlm.R
0c5f421ee4d689df2b822ae067c52ce9 *R/LimmaBackgroundCorrection.R
1dc087f307bc8b73ba9cf3d2b2f1415a *R/LinearModelProbeSequenceNormalization.R
8f5fc8a480e242419242d1edcd674194 *R/MatNormalization.R
79491d1dd4a7e7cbcf3e5aef9d3b0569 *R/MatSmoothing.R
ab8305a6d637586411d3fe1300a8d2ca *R/MbeiCnPlm.R
ed033d6421ec019f1fc7f900423fdc3b *R/MbeiPlm.R
98a9e5b2dd5639daa0c685bd62956101 *R/MbeiSnpPlm.R
29c438bf9dfd37af3e04093ad0fe3eea *R/Model.R
51911859d289f74f76199ab1434b62a6 *R/MultiArrayUnitModel.R
06bdfacf4606480b7a1abbd35cb50e60 *R/NormExpBackgroundCorrection.R
9a0648000e32e17aa7bcdf5a0a7a6f6f *R/OpticalBackgroundCorrection.R
9388086af14d2145806a908149b6fa41 *R/Package.XTRA.R
03cee558848ac45833eec862dee27418 *R/ParameterCelFile.R
1cfaa8cdd610af51dfbdf096fe58e6f8 *R/ParameterCelFile.extractNnn.R
d5da6c0f6b2ca2f02d0ca12786c189b3 *R/ParameterCelSet.R
db28366006be48eb6417d35bd1f259cc *R/ProbeAffinityFile.R
e17249275cd130c8c3151d169891c176 *R/ProbeLevelModel.R
7cf825f2ffe17c4ff275369c5bd0d428 *R/ProbeLevelModel.calculateResiduals.R
a5a54c3b68aa06eefbfbf749b9218d36 *R/ProbeLevelModel.calculateWeights.R
41c1c261946328afc18cc4965e6f94c2 *R/ProbeLevelModel.fit.R
f5d3a745926e64fe5914e9056a115d09 *R/ProbeLevelTransform.R
1061b80c2a62eeb516e8d4f65b5cc2fc *R/ProbeLevelTransform3.R
20e0c493e71fa681c664f91c407dfa42 *R/QualityAssessmentFile.R
e6950cee2ad9f3aa4367fcd3a07f1b1b *R/QualityAssessmentModel.R
cd4ad27696391d0cfc86c36240380680 *R/QualityAssessmentSet.R
07e440c23dcd5a0237fd455baf676837 *R/QuantileNormalization.R
2aef804fc3eb92f45bbcbf24cb3d6b22 *R/QuantileNormalization.xtra.R
7b8198d75d65ccccfd54eb9ef8f0de55 *R/ReseqCrosstalkCalibration.R
30d10af4f2cec2018b00c8afbfaa7b5c *R/ResidualFile.R
2d3b64b64bf06f6b6a0dfdc456ed6fbe *R/ResidualSet.R
2faa91043d274f873db136fa23bdf453 *R/RmaBackgroundCorrection.R
ecf7f6b7c504251449179102670a4ddc *R/RmaCnPlm.R
9d8c35780221a35a89ecee0826747566 *R/RmaPlm.R
122aa7007404368602d3918000c0f6e3 *R/RmaSnpPlm.R
de36d79557da2a2c7c20c6cc6358bc7b *R/ScaleNormalization.R
b57371435b7db7634539a604ee2ff7b5 *R/ScaleNormalization3.R
c6b0e8fdc0856856cf29386cd0876e8a *R/SingleArrayUnitModel.R
7d431bf5033b22f9ab26ac50703c8a5f *R/SingleArrayUnitModel.fit.R
cf5ac8a589de9b90fa6bdc1f939ce5ba *R/SmoothMultiarrayModel.R
b135d132d4596eb3062d6d41ab732ca2 *R/SmoothMultiarrayModel.fit.R
8415a030c231c59f069313f2ade43851 *R/SmoothRmaModel.R
271a88f24f0d8d421b99539576488f5d *R/SmoothSaModel.R
b7c205621c4f27c9abf9f4ed416717e1 *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
4c2cc859d822dc53828ab6b28c9826df *R/SnpChipEffectSet.exportTotalAndFracB.R
0ca79b849d7dd82210a62104a4610191 *R/SnpChipEffectSet.extractAlleleSet.R
d759c15129055b07d1b8eb491b4b4570 *R/SnpChipEffectSet.extractSnpCnvQSet.R
2dcba4bbb33cba21a21c3bc72f2e9a18 *R/SnpChipEffectSet.extractSnpQSet.R
96051d1307cffc2ebed2e01ba820f1a4 *R/SnpChipEffectSet.extractTotalAndFreqB.R
db95f57d9a491d9059eb1be07ef8b01c *R/SnpCnvQSet.extractTheta.R
516d2c40783bd818503f6246e27aa6f8 *R/SnpInformation.R
401fecb21ee3ee6f4397e44f1ee97ed3 *R/SnpPlm.R
ef3ab4851bf81402487ab84f1d9e2d73 *R/SnpProbeAffinityFile.R
37b94dd8917eefab71dc04539758240b *R/SnpQSet.extractTheta.R
a46be25242513a6a98ff5bf621ed02ba *R/SpatialReporter.R
54f1e4df72b224cf123654f390469eb6 *R/SpatialRowColumnNormalization.R
790a367320e8621a09e4b50c718078fc *R/Transform.R
cac6947c5a251c3730170f51095a9947 *R/TransformReport.R
dee8e1f1478cde2fd6a6bdee240505ff *R/UflSnpInformation.R
493450212e39eb374f38f07d5ecddd2c *R/UgpGenomeInformation.R
03079a9c0f419d7e86cf43c5493bb495 *R/UnitModel.R
3231f9f2fcfcc905d6d2a2374243cea5 *R/UnitModel.fitCnProbes.R
3c1d07a50a72a7e80e3a97b33eb7ca13 *R/UnitTypeScaleNormalization.R
4fd56e715609e6794166edcae4c3f668 *R/WeightsFile.R
b831aa1fc4afb5f972664117cff05697 *R/WeightsSet.R
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