1301f2e829ec8d952a058b502410ddb1 *DESCRIPTION
5df13a843527aba142a61b72e01d2fe1 *NAMESPACE
b35effcf234ce60673fe8636039516de *NEWS
5b3e0291bcc049d9ada9005162c5259a *R/000.R
6f483cc1cd9c7fb9e1c0636c988af7ac *R/006.fixVarArgs.R
2a0d6e51756d2cdd3197ab115963b6ea *R/008.BioC.R
8cdfd28366738a9e4daf107bc08b04e8 *R/009.setup.R
8edbdec60a690885a24d04ec69425c85 *R/998.AromaPackage.R
ba95f377ee43ef3247e9fba983df14a9 *R/999.AromaCore.R
b77cf24da3cf28b856623a6d4171161b *R/999.DEPRECATED.R
5b9ea216c47a57e772308c8d17cfd10e *R/999.NonDocumentedObjects.R
b2040f35dad685b10d6b5dafb1400a26 *R/999.package.R
63415c1d9646302b7cef5e63de682f11 *R/AbstractCNData.R
877ee174d481c7d54aaf5f3b22659023 *R/AbstractPSCNData.R
ba0f94f57757548b2dd560685260f0d4 *R/Arguments.EXTRAS.R
b0c051f205efce5d4e9c5a2991b060a8 *R/AromaCellCpgFile.R
d8281490389b2e19f3ee235285078384 *R/AromaCellPositionFile.R
0031436fc4a046557a4ad2f2ce5ce4fa *R/AromaCellSequenceFile.R
ebf87178f612a40ff8b6cac76875669c *R/AromaCellSequenceFile.REPEATS.R
e2fabbeb403d8adf0328f04a3c0b87dc *R/AromaCellSequenceFile.SNPs.R
c3bf4f363fb18a95c81b1a271995df75 *R/AromaCellTabularBinaryFile.R
775c6af6394ee04776fb45efc3a62101 *R/AromaGenomeTextFile.R
31a921512f793ce85960ae68d296b0aa *R/AromaMicroarrayDataFile.ATTRS.R
64951a7281747a27b8d6ae30593cc353 *R/AromaMicroarrayDataFile.PLOT.R
f9c325122aa417862dd16d6e92c46c58 *R/AromaMicroarrayDataFile.R
1fa942d2968dbea157c833da00f3e412 *R/AromaMicroarrayDataSet.ATTRS.R
30e5d36c228971a67f18a2b7d4a0fcdb *R/AromaMicroarrayDataSet.EXT.R
089d24655e96e098398a518cfbeedf9a *R/AromaMicroarrayDataSet.R
748776665cb771cf9da496baa2fe32f5 *R/AromaMicroarrayDataSetTuple.R
410e97b770ed7a24c62a0ed9c4a7c641 *R/AromaMicroarrayTabularBinaryFile.R
f3761cff801f08e1b88030ab36ef4a29 *R/AromaNnn.getRootName.R
9cf8a604f535a06118513fc0747b85bb *R/AromaPlatform.R
a622feacf9e03c3074bc0d5e3d4bfe40 *R/AromaPlatformInterface.R
9dff22bbdeace5c36bc1e483cc75276e *R/AromaRepository.R
1990c30ae579ea84bb990930ac97961e *R/AromaSettings.R
4f1df419b1f0ec1b06b94e35683f8e61 *R/AromaTabularBinaryFile.R
ed2f10d13b742b51585981c1af6d1077 *R/AromaTabularBinarySet.ATTRS.R
3b3e5c4b00f2dd4ab02e918eab064944 *R/AromaTabularBinarySet.R
7ee4e513fe2a975b16cce0452550bbbd *R/AromaTransform.R
78d4c0d4a346ef04c943aa15d11d6caf *R/AromaUcscGenomeTextFile.R
ec5ab3073ff140d3981aa607fb94fd3f *R/AromaUflFile.R
2bf2fce346519c8120db7d46d09d11d6 *R/AromaUgpFile.R
86f133577631d59208c60c4745c7e77d *R/AromaUgpFile.plotCoverageMap.R
338f6af564f66a29638fe47a0db2f2e7 *R/AromaUnitCallFile.R
26be1eaf64d917d1d2177dafb5ab388d *R/AromaUnitCallSet.R
83a195e5626d81f15b0dd87e358a7c83 *R/AromaUnitChromosomeTabularBinaryFile.R
372b4d3ca6d5481cd87a40b05a70b7c9 *R/AromaUnitFracBCnBinaryFile.R
c0ad0a43e529ccf49b61468b539a90af *R/AromaUnitFracBCnBinarySet.R
91021ddbfa5bced2f1732ce692e303db *R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R
d5c1a0f084f0e5e9776b13de75c8e199 *R/AromaUnitGcContentFile.R
9199f476f16d5bf01ec8d1430c672abc *R/AromaUnitGenotypeCallFile.R
512c081b0740ecd03abee043ffe23438 *R/AromaUnitGenotypeCallSet.R
b20742f88aca1c4bf4cdff1b0f0ae79c *R/AromaUnitPscnBinaryFile.R
90ad69d3200c4891924be9f784e40874 *R/AromaUnitPscnBinarySet.R
6bb0fb4635c91892049ac6476c66f427 *R/AromaUnitSignalBinaryFile.R
4498bc457ba8f7631ca7f5bea920caf6 *R/AromaUnitSignalBinaryFile.writeDataFrame.R
21d9e0d2019ad996c923d70b57580b1e *R/AromaUnitSignalBinarySet.R
e3e232e0d81b70f2788fddb15d916e57 *R/AromaUnitSignalBinarySet.writeDataFrame.R
9cc6a857ac4fe017bd2564e75dfb543c *R/AromaUnitTabularBinaryFile.R
42c708f856ac1c79e0de8bec816ceb7d *R/AromaUnitTabularBinaryFile.writeDataFrame.R
26dc1262be72a220e60d70269a62ef75 *R/AromaUnitTotalCnBinaryFile.R
3bddcf4a00cb6c51ecc18818769cdf08 *R/AromaUnitTotalCnBinaryFile.extractPSCNArray.R
224a7be6c1abf237d59fff9ce290537f *R/AromaUnitTotalCnBinaryFile.xam.R
dc42af5346adafa3cb252a6b8c0bb19b *R/AromaUnitTotalCnBinaryFileList.R
427c93be8dac9e29fbbcc94cab742117 *R/AromaUnitTotalCnBinarySet.R
78671b760800197c90eec9e0ee917c97 *R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R
c479b796502fb298431c23bcaab2b534 *R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R
0715413f06a5d7f4379709fa1a6baa29 *R/AromaUnitTotalCnBinarySetTuple.R
66085cbc6513f6f1aaff29b7e1dd3bac *R/AromaUnitTypesFile.R
7044fdb90a657ab29a3591a3ee373552 *R/BasicObject.asThis.R
a43d16f5e37d34f996b666702f282ff4 *R/BinnedScatter.R
3b9f06859196271af36ecc1b5c295a1b *R/CacheKeyInterface.R
fdceb61f80d0d8697237e6da18dba3b1 *R/CbsModel.R
80d6883eccd504d7a344b8f74b036890 *R/CbsSegmentationDataFile.R
5872b8b4a0abf0d3db64d0b78f488de5 *R/CbsSegmentationDataSet.R
7704a9b143456eaeef1bb0f41f840100 *R/ChromosomalModel.R
a570674e4c3d9cb5d6aeeefc670bf96e *R/ChromosomalModel.drawCytoband.R
ffbed1fc6288669c610edbf6eb79bfec *R/ChromosomeExplorer.LAYERS.R
c019babeaf3242207c32889f8027a6ff *R/ChromosomeExplorer.R
b73200052e94f8c4f7d9c3102caa235c *R/CopyNumberChromosomalModel.R
557a3b2cea21738f1a47d23e1e29e27c *R/CopyNumberChromosomalModel.newPlot.R
8c21a23a96cee6a79f3168527b4d025f *R/CopyNumberChromosomalModel.plotChromosomesLayers.R
8551326b6e48e28a53225b4b965c082b *R/CopyNumberChromosomalModel.plotFitLayers.R
bb6f3b7cf9306a27a13c4da96d94681c *R/CopyNumberChromosomalModel.plotRawCopyNumbers.R
209623d223f824e7cc5b3a92260540cc *R/CopyNumberChromosomalModel.plotSampleLayers.R
807f80f70c9251f4f4bdf09dfca757aa *R/CopyNumberDataSetTuple.R
dee441f913afc039e4876c07cd7ae4d3 *R/CopyNumberOutliers.FOREIGN.R
56f007e5434e7ab9d7cf4ed50eed8bd3 *R/CopyNumberOutliers.R
398d8df05f13610f05d99d6e88bc5c1c *R/CopyNumberRegions.EXT.R
210d9ecef32fb285703822f4c900efa3 *R/CopyNumberRegions.EXT2.R
8337159cf85fa0d44ceb062aef9ea639 *R/CopyNumberRegions.PLOT.R
b24cc179eb5f478b02183fe0d4558ff2 *R/CopyNumberRegions.R
7f0cb3c8441f910bfc00896307af73b1 *R/CopyNumberSegmentationModel.R
ff8759fb2e2d69e496638e638c3d6279 *R/CopyNumberSegmentationModel.plot.R
ee33978f0573743cffe1d7de44988f46 *R/CopyNumberSegmentationModel.plotCopyNumberRegionLayers.R
e4cb9bc77e7aa3f09cc0f2ac35fe8003 *R/DNAcopy.EXTS.R
4051948de667b3f1dc6bf291b6d9ea53 *R/Explorer.R
1ad70a1d14a8dcf325f167acdffc0be8 *R/FileCacheKeyInterface.R
d16c29f1ecc56cf0a9af1515227c35ac *R/GLAD.EXTS.R
ee5dedbbfc510fb5f274feb4f92f6df0 *R/GenericDataFileSet.getParentName.R
3f6cf03559d713c37387c67bb24e14e1 *R/GenericTabularFileSet.calculateAverageColumnAcrossFiles.R
61ba6d32226632a77495683e0168bcf3 *R/GladModel.R
b5bca462f599b89e1b559e705e0b146b *R/GladModel.onFitAddGenotypeCalls.R
75580eda3d4edc20b5dcebf2270d0c65 *R/HaarSeg.EXTS.R
71f7b27f7a1fad8952e1f9c3c84fa3f8 *R/HaarSegModel.R
07f7dfef56ca865f11a8870328b505a7 *R/Image.EXTS.R
76fac21f724406941852903f980009e8 *R/MPCBS.EXTS.R
dc9adfe52cf08955528b1695d1c2cb58 *R/NonPairedPSCNData.R
c9c9f5da3bb011dc328d2ed7e5fcc5ae *R/PairedPSCNData.PLOT.R
7e3b5692fb5bb24b47888d9454a6a286 *R/PairedPSCNData.R
f1b418065ff6c109ae6b6bfcecfaa32b *R/ParametersInterface.R
aeda31b9ddc7d4250b19adcf825b43c0 *R/ProbePositionEffects.R
99cc6c838c33af8638bc09316bfd437f *R/RasterImage.R
26e725b28b2201358ef82ed9c9577d89 *R/RawAlleleBFractions.R
3d27fc2df0a9d3e1fa1b329056410b51 *R/RawCopyNumberModel.R
b67a87f04208c48d9cf6c8d7684addfc *R/RawCopyNumbers.R
fbcef0c14a456bbad71038a81b800e86 *R/RawGenomicSignals.OPS.R
51220e8593d0999f2e27bd082cbf12eb *R/RawGenomicSignals.PLOT.R
eef6f24268ef743807206ee309be9e5e *R/RawGenomicSignals.R
430d91d38a5bc6a7252a976085bdf46d *R/RawGenomicSignals.SEG.R
ea57ade0d2ce46427f0301bb59a4d647 *R/RawGenomicSignals.append.R
0035e9fb6e5c413424433f65cdd0608f *R/RawGenomicSignals.segmentByCBS.R
737d36ac3fa6d89f1034097a4687ce12 *R/RawGenomicSignals.segmentByGLAD.R
2deeb901ff894b1c0db49b06e2b0badc *R/RawGenomicSignals.segmentByHaarSeg.R
be3c21e241aba96abc7e00e54738ccc9 *R/RawGenomicSignals.segmentByMPCBS.R
9d98652f3825487f83533207e12acc61 *R/RawMirroredAlleleBFractions.R
4e077b9c79d24ce79ea7377302409750 *R/RawSequenceReads.EXTRAS.R
c7b6c3354273fd44efb1cabb24e0f6fc *R/RawSequenceReads.R
99f751ba3bfb4fdd3e78e31781f4a4c7 *R/RichDataFrame.R
d4a6e8e9a6b2eb8ac333b593f802e9bf *R/SampleAnnotationFile.R
c611c3e231bdd032585794b18057695e *R/SampleAnnotationSet.R
9d9841a29c5d1fcf38b5be0d2e4ba2b4 *R/SegmentationDataFile.R
a94d4604e9e13188062cb8d61d283895 *R/SegmentationDataSet.R
8bce5d582c24ddb6b4ed32d0e4b5f76f *R/SegmentedAlleleBFracions.R
50b028edeff0706e8872e45c32a7d323 *R/SegmentedCopyNumbers.R
644a1825a5d46bb778e9f1876fffb0ee *R/SegmentedGenomicSignalsInterface.COLS.R
75dde6da848975d0a4875ed1f92165ab *R/SegmentedGenomicSignalsInterface.R
56eea30b020a0e53d2f573e13ce2e2e0 *R/TextUnitNamesFile.R
729afbf031f06e851dd0c98b768fdfa4 *R/UnitAnnotationDataFile.R
3b5ef087d62981f7376c134586634e34 *R/UnitNamesFile.R
564ea479cf7248e0c927f15f5eb01c58 *R/UnitTypesFile.R
0b8477cdc3cbf949b2b12fdc917933cc *R/backtransformGenotypeCone.matrix.R
ea7dd4032407fbc3e58f92fe19d39a5e *R/backtransformMultiDimensionalCone.matrix.R
444363e414255d2e40188899948ac989 *R/colBinnedSmoothing.R
ee7ba3a665bfa8d50cfb993c8a66133e *R/colGaussianSmoothing.R
a936ff30815cb99fe4aab26869ba8b0c *R/colKernelSmoothing.R
fc9f549290373a0c029ca36ce7fc846f *R/convertTable.R
3894c08d621848c05980062a6903688a *R/doCBS.R
8deda3d04295c897d86a0ba8e448a668 *R/drawCytoband2.R
94feeaaaa671ad3080873a61933c7410 *R/findAnnotationData.R
1596fd6b0fe890c8190c778745aeca8c *R/findAnnotationDataByChipType.R
32f4fb84355cf5018549c206a7bb91b2 *R/findPngDevice.R
5800378c5a25c2e3f2a5aee1769c7128 *R/fitGenotypeCone.matrix.R
336503c483ab16eeda413e26f2d76678 *R/fitMultiDimensionalCone.matrix.R
73e78823f52d9092604e3c3bf9e0669e *R/fitSplineBlockPolish.matrix.R
e64c7c11f7fe617c9bbd14e6bf0b90eb *R/fitWHLAPLM.matrix.R
15e7283426d1acdc098b7046ff102655 *R/fitWHRCModel.matrix.R
017cb2d392e1074266ff83513d059989 *R/fitWRMA.matrix.R
e86461b9085da6bbe02870181e7de635 *R/getAromaFullNameTranslatorSet.R
f2d5120b89c80823746fd60f93f9a708 *R/getCommonListElements.R
60fbbbc0a8c9467fa870de2f7550f323 *R/getDeviceResolution.R
0ba8739126fe6bed418e75a37b315bec *R/getProbePositionEffectDesignMatrix.R
fae4b51a0c10b993ef8b875cf0d6dd16 *R/kernelWeights.R
e4d82ee6bf532d9b0a7cfc85ac0f6b7d *R/lapplyInChunks.R
c7ef0ea6c83f018e3e4b861c5a3fb615 *R/library.patch.R
fbc82ab641f5193846051da964fe4a06 *R/locallyUnique.R
8a460af06ddd73563d26f6930426aef8 *R/matrixBlockPolish.matrix.R
500733154f5ed044abf8eb1bd33af661 *R/mergeBoxplotStats.list.R
ed936047c2ce024163bd4ac08d80a4b1 *R/norm2d.matrix.R
d4118e3bacee85f345702edcea442dce *R/normalizeGenotypeCone.R
e8c4b0f690fe13066583c24438e59369 *R/private.Machine.R
107f9bbb4ffc52fa8266cd2ddb7f4d02 *R/processTime.R
298d32badc7400da2d83320aa304fe24 *R/profileCGH.drawExtraAnnotations.R
50ce069381f4ba1d5622c62c8dc48c49 *R/profileCGH.plotProfile2.R
41dddbc5214e9f59c306aca62bcac720 *R/profileCGH.plotRawCNs.R
332068b29cc2f25e4339d3137863e12b *R/remap.R
9ce035ccdbd1aef596d21a8a299a898a *R/requireWithMemory.R
049002856d48452a7953be4757497b7d *R/shakyText.R
093c301c3e64d1808bbb77d5ff977e14 *R/simpleXml.R
32943e20bbb4117ded3feb17cf5b7776 *R/smoothWRMA.matrix.R
a2aaaa1f6ffde7b11ac6ab88bedbe37f *R/smoothWSA.matrix.R
8735b6a8c6e8e7b292acfc6ab12b5168 *R/stextChipType.R
35051e75216c33d3021d97c2dd3be439 *R/stringTree.R
76d2433012b7a038766771679fb3e7aa *R/transforms.R
5d70959a9e051a5666c0524ad97022d9 *R/utils.R
dfd8e781870d9ca7d305462d45b044aa *R/yellow.colors.R
d5aa2e30591d83b4285465096c7d2e06 *R/zzz.R
d570bca976776301e874467a4dcfe01b *inst/annotationData/genomes/Canine/Canine,chromosomes,UGP,HB20100822.txt
0bfaac041f78c030c78315b686eafa1a *inst/annotationData/genomes/Human/Human,chromosomes.txt
6e9d640871de559bdcc3c4158a11b353 *inst/annotationData/genomes/Human/Human,cytobands,hg17,GLADv2.4.0,HB20100219.txt
966b4e1431cd7834849e155eeb56b07e *inst/annotationData/genomes/Mouse/Mouse,chromosomes.txt
bad6afe381a3f46e5e51ae347d1a4e5c *inst/bin/nohupR
4a363995e70d3a06bfd88fb659e57587 *inst/reports/includes/css/ArrayExplorer.css
b2cdbe19a55b0bc4deb690f6273aa23e *inst/reports/includes/css/ChromosomeExplorer.css
ebc5cda694d0cb29516f94901f679c16 *inst/reports/includes/css/R.css
aaa5d87d7bb4fe42bc0d570110c816f3 *inst/reports/includes/css/figures.css
3cd9c200e96a40470c7755de2f81c57e *inst/reports/includes/css/rsp.css
03ce3dcc84af110e9da8699a841e5200 *inst/reports/includes/images/indicator.gif
50c5e3e79b276c92df6cc52caeb464f0 *inst/reports/includes/images/indicator_medium.gif
b3f56b4e9ef53fc8ad8f57b28c534397 *inst/reports/includes/images/pixelWhite.png
eece49fb8c8dd892cd582e38f42958bd *inst/reports/includes/js/ArrayExplorer/ArrayExplorer.js
d444a44670c6beec0337a7c518f401da *inst/reports/includes/js/ArrayExplorer/HISTORY
649ebaffbbef57c929227572bd977231 *inst/reports/includes/js/ChromosomeExplorer/ChromosomeExplorer.js
722764c8d8cb081e530379f1b41a20d7 *inst/reports/includes/js/ChromosomeExplorer/HISTORY
91d18d62d64b49439ff186f63685d337 *inst/reports/includes/js/ScrollImage2d.js
ec9a59af1b6880be38e3b60214ddae96 *inst/reports/includes/js/Scrollbar2d.js
44c00c3f7b1359398b47529b2ddb2954 *inst/reports/includes/js/Webcuts.js
6f5d3146dfb386be84c5baed6807f04a *inst/reports/includes/js/domUtils.js
93c42caa183c27206be4ac34df14b8e9 *inst/reports/includes/js/require.js
a13014d238fd12b5a5f4a971f6fd27e9 *inst/reports/templates/html/ArrayExplorer/ArrayExplorer.html
721346fa44342eb9316a984451a4fb84 *inst/reports/templates/html/ArrayExplorer/about.html
524a72cb297fdd198f05a37b479f8873 *inst/reports/templates/html/ArrayExplorer/help.html
92ad470c28973f80426746b2c24c67a7 *inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer.html
31f887f10c19f4dc51bb398d434e3e6f *inst/reports/templates/html/ChromosomeExplorer/help.html
a6d9db6dcc63e828e237d905aeec00f7 *inst/reports/templates/html/ChromosomeExplorer/index.html
05cb8dccdcd82c31eee2a55fb5772e2d *inst/reports/templates/rsp/ArrayExplorer/setupExplorer.js.rsp
49633d9d403d51a9a89a633ee949680a *inst/reports/templates/rsp/ChromosomeExplorer/setupExplorer.js.rsp
70d9d9df68ffb185195227a6d0e576d0 *inst/testScripts/fileFormats/acf/test20090105,acf.R
f85a505aa51f7f231fac35fa50ec2e86 *inst/testScripts/fileFormats/acf/test20090107,AromaUnitGenotypeCallSet.R
0ae43085c2078c13d06885d278082c92 *inst/testScripts/fileFormats/acf/test20090518,acf.R
1ccbad88501dfa71554c589d1ecd7c27 *inst/testScripts/fileFormats/acs/test20080804,acs.R
3a9db673adf694a93e56c7541aecf47c *inst/testScripts/system/CnSegmentation/test20090510,SEG,weighted.Rex
a68f7649d266b2c43ce2daf5574dee41 *inst/testScripts/system/CnSegmentation/test20090510,SEG.Rex
cd97fa95e82b4653c17885a8af25f4ba *inst/testScripts/system/CnSegmentation/test20100222,SEG,symmetry.Rex
1ba165622d4c11de49db5a203fff7c90 *inst/testScripts/system/RawAlleleBFractions/test20090510,FracB.Rex
53b6c894b9dff13e00b2899be512263d *inst/testScripts/system/RawGenomicSignals/test20090510,Ops.Rex
cb4e8df20db470b31462cb585ce4d480 *inst/testScripts/system/RawGenomicSignals/test20090628,binSmoothing.Rex
a36ab22376918586646237be90f32dc6 *inst/testScripts/system/RawGenomicSignals/test20090628,binSmoothingByState.Rex
a4ccafae7719a60abc5ac2d8a07e57dc *inst/testScripts/system/UGP/test20090508,UGP.Rex
f90abcf41069615904d7fc7bed10f454 *man/AbstractCNData.Rd
ffba5545d04ec1f3839631930e1c454f *man/AbstractPSCNData.Rd
caf89ae3642d876eca8c518bd54c9a01 *man/AromaCellCpgFile.Rd
b934825640f2adee1942164c44d84550 *man/AromaCellPositionFile.Rd
18c9d259d3baaf5a777cb54745804a49 *man/AromaCellTabularBinaryFile.Rd
3df15ec22a4e9ee35cf43f1ce230d91d *man/AromaGenomeTextFile.Rd
7b26c12d617d09172a5d3bacd65a91ad *man/AromaMicroarrayDataFile.Rd
6fd0542fb19266c3f955ef6c10f8b23c *man/AromaMicroarrayDataSet.Rd
2bfef94af7c46efefcde975570accd75 *man/AromaMicroarrayDataSetTuple.Rd
46bb3e93715d660c325625bbee9b48a2 *man/AromaMicroarrayTabularBinaryFile.Rd
248c4345f7d9444ed8a731bf5be77d78 *man/AromaPlatform.Rd
30ff629c52b715465808cbb8e1b41363 *man/AromaPlatformInterface.Rd
c7072145308b097b80212e893e122a38 *man/AromaRepository.Rd
d60af633aee2a71522267f254dfb55f7 *man/AromaTabularBinaryFile.Rd
da4130e7872505d72935a9728a60eff1 *man/AromaTabularBinarySet.Rd
8281cead74e93fdcdc18ab05433b4113 *man/AromaTransform.Rd
d497c4f2fae194ad443da0ba7e61f542 *man/AromaUnitCallFile.Rd
549411bbac3d89367c363b202c973912 *man/AromaUnitCallSet.Rd
51e3e43beb0de25ac0e5d62f51ec1c54 *man/AromaUnitFracBCnBinaryFile.Rd
e011acda24148875eae0a0ccd9aa4eb4 *man/AromaUnitFracBCnBinarySet.Rd
c63355c149170e07a0b5dc5e86f96286 *man/AromaUnitGenotypeCallFile.Rd
c814919bcea8cf19ab175640f9fc9c98 *man/AromaUnitGenotypeCallSet.Rd
0d19b1947b6a360e855032da89daa285 *man/AromaUnitPscnBinaryFile.Rd
791a0283c8e6fc6554dc330d3ff4081f *man/AromaUnitPscnBinarySet.Rd
d72a99fb314d06df6b3dde0aaba9bed3 *man/AromaUnitSignalBinaryFile.Rd
f3b6f76f1a988ea1ea0895949e6b9d7e *man/AromaUnitSignalBinarySet.Rd
c3d47a9ac5ad13e8acc9c050db83e9fc *man/AromaUnitTabularBinaryFile.Rd
46825f7563e864cdea29420adf61c788 *man/AromaUnitTotalCnBinaryFile.Rd
fa1525b7d51ca21a9c40e298c5ca6c07 *man/AromaUnitTotalCnBinarySet.Rd
9a154f3f10bc6db90a53292b2b360885 *man/AromaUnitTypesFile.Rd
07f27b39eb1bdf68f21096d8991e6754 *man/BinnedScatter.Rd
0f1befda8b0e1e9a051339cd8956ae9b *man/CacheKeyInterface.Rd
f696c000e2b1b8ebc1b12f0a9d998e62 *man/CbsModel.Rd
7986970124f3cae86589e69a772f01fe *man/ChromosomalModel.Rd
45729d73e8de515c5aa6b7b979dd7fc9 *man/ChromosomeExplorer.Rd
13b0f7519cdf26bdefe35ec2526e81ad *man/CopyNumberChromosomalModel.Rd
1270798e47ece7fc59ec5bf563c88f65 *man/CopyNumberSegmentationModel.Rd
da9705c0dc4d9d904a56640fca876a43 *man/Explorer.Rd
140695134876b77d6de20695c512cb92 *man/FileCacheKeyInterface.Rd
61a4323a2b88f75a052b02af384ddec6 *man/GladModel.Rd
05eb1425d6b890c5d2aff942aa1e8de8 *man/HaarSegModel.Rd
afed9244e2cd10c42bdf7cedfef5a2a2 *man/Non-documented_objects.Rd
3ec9f40966a8903224e6d753e9f7b5f5 *man/NonPairedPSCNData.Rd
990dc3f44076e5344610e17ed8b3cdd0 *man/PairedPSCNData.Rd
361e38df7b6f6b79f5c03ce0f0c8702d *man/ParametersInterface.Rd
90efe92407849672ef98690af0e9e794 *man/RawAlleleBFractions.Rd
9773d372cee5c47394a6d4528ddd2a9e *man/RawCopyNumberModel.Rd
8478ca54bbb4759bfc2651f0037902e9 *man/RawCopyNumbers.Rd
559a0eeaec59a2ba378e66c2fa2cc637 *man/RawGenomicSignals.Rd
5172ed620622a9bf963559510c831b93 *man/RawMirroredAlleleBFractions.Rd
2fc35438734571d74a7e295ae2c9e447 *man/RawSequenceReads.Rd
ba570db63f526fbe972cc43834f8a438 *man/SegmentedAlleleBFractions.Rd
ae4b599e90d18fd702e1bbcb8fcb19b3 *man/SegmentedCopyNumbers.Rd
ee63255e7c769bc5603740b6e818e120 *man/SegmentedGenomicSignalsInterface.Rd
27291dffba5f086656ae75a989167db1 *man/UnitAnnotationDataFile.Rd
d5d4de0e39e56ad2c87b186210dac53a *man/UnitNamesFile.Rd
476bddacdef94f94bb9fcacb2fd22139 *man/UnitTypesFile.Rd
3d8f83c334925ccc6e7109e84594323d *man/allocate.AromaTabularBinaryFile.Rd
8ad30456383941f67fbf57b5cc611b7e *man/aroma.core-package.Rd
5e18ad681bcda0262fa58f3ed01e8068 *man/as.GrayscaleImage.matrix.Rd
89d450254dd68f23c882db9fa6f0a693 *man/colBinnedSmoothing.matrix.Rd
18bd75e84feb4810526bd3d13c056d3a *man/colKernelSmoothing.matrix.Rd
a15f5c10b8ff20e51df4f5913778ca43 *man/display.Explorer.Rd
bc45901abc6e41db3f67481e2956e7e0 *man/doCBS.Rd
d22420ddaa560cd6759efa62fe7543ac *man/downloadChipTypeFile.AromaRepository.Rd
da6328201409ad25e3310d22e73cd061 *man/downloadFile.AromaRepository.Rd
78e2a1879d39f03d1361966d647e011c *man/estimateSds.CopyNumberChromosomalModel.Rd
dab124d5a7c1fe1d9898b9b6b82ad29d *man/estimateStandardDeviation.RawGenomicSignals.Rd
7dbf49a78c2fc9376912c9da269de843 *man/exportAromaUnitPscnBinarySet.Rd
3e5a98f785f24777615f47d229c36d6c *man/extractRawCopyNumbers.CopyNumberChromosomalModel.Rd
9a285ab9f942b136dd2c07b15047b4d5 *man/findAnnotationData.Rd
152a0c5c59c1dc69c716e282991fcb42 *man/findAnnotationDataByChipType.Rd
b5826c79c23f2670ad9f15a35bdb473b *man/findFilesTodo.AromaTransform.Rd
0d436d63a79dc18fc00954a6e14df853 *man/fit.CopyNumberChromosomalModel.Rd
fb5699e4026677ed7f2a1bd5b5ed4089 *man/fit.CopyNumberSegmentationModel.Rd
8756cdcadc2048e2922e334debafe0b0 *man/fitGenotypeCone.matrix.Rd
b2179e875babc9c4ad738066b31909c9 *man/fitGenotypeConeBySfit.matrix.Rd
4772691ab4f3f0bf689a8f93cb18a324 *man/fitMultiDimensionalCone.matrix.Rd
aa376507af267cae4503661533b82180 *man/getAlias.Explorer.Rd
91f4c5e721688c96de9dd4ebc5508aa2 *man/getAromaPlatform.AromaPlatformInterface.Rd
cae2cff6e8ac32bb57290460445c1568 *man/getCacheKey.CacheKeyInterface.Rd
a7624e852f589b5efd66eb817090a544 *man/getCacheKey.FileCacheKeyInterface.Rd
94f6e65e7186b2eb147cc2c092051597 *man/getChipType.AromaPlatformInterface.Rd
c62793730eb784b636235c8cd03621ec *man/getChipType.ChromosomalModel.Rd
79ac86384a40eee47a3a0b83d66e7184 *man/getChromosomes.ChromosomalModel.Rd
df2c5c41cbb14a651b47977844d62205 *man/getChromosomes.ChromosomeExplorer.Rd
41a451dd4656282562fcb5a85b4f4fdf *man/getFullName.AromaTransform.Rd
0216732f921a2eaa866506d2c0d17ae4 *man/getInputDataSet.AromaTransform.Rd
63cf2b3c220dc55cb83976c5c67061de *man/getModel.ChromosomeExplorer.Rd
26ad06c89c32437dc543b0bcec0c8e58 *man/getName.AromaTransform.Rd
c07823091aecd469d1e00bc8a66b80e3 *man/getName.Explorer.Rd
d204d9a7c2cba3818f2271fd5e62fd57 *man/getNames.ChromosomalModel.Rd
90320564af0e00bbb3984dd5f16a0d22 *man/getNames.Explorer.Rd
59fa1a611ac957b766ec63d794d0e2b7 *man/getOutputDataSet.AromaTransform.Rd
fdc102de0f57529762c95c46c86b8c44 *man/getParameters.ParametersInterface.Rd
60fade3c68e94f0c83166dda0d902303 *man/getParametersAsString.ParametersInterface.Rd
7c6ba93a9704181b6197a6d2bd4215e9 *man/getPath.AromaTransform.Rd
7122408a82d99050a4075b1792297c48 *man/getPath.Explorer.Rd
62abe57ea2fdf5b5e3b0c060775f1c2b *man/getPlatform.AromaPlatformInterface.Rd
afc3244e5a73a4f10a540be9f4553748 *man/getRootPath.AromaTransform.Rd
a555abe7f03d4a1fd4e89660e7b4da6a *man/getRootPath.Explorer.Rd
6a9c3edc2a5522fe69f4a0c249431155 *man/getTags.AromaTransform.Rd
e71460e6ef32db0f1b84f3ebadf095be *man/getTags.Explorer.Rd
0c7ad6638abc7a86a56deabb9b106526 *man/getUnitAnnotationDataFile.AromaPlatformInterface.Rd
4de2d2f22bd78fc0d8c15e2956be63d1 *man/indexOf.UnitNamesFile.Rd
23e3488f3fe0af2c26336d26abfb6831 *man/isCompatibleWith.AromaPlatformInterface.Rd
0de9e3cafc1e764c22df7e22e882b10d *man/isDone.AromaTransform.Rd
d4f77ad1878ce2543f4e9c50dd8c57f2 *man/listFiles.AromaRepository.Rd
74b011e8f05e8adb942bebc7ee6a84f4 *man/matrixBlockPolish.matrix.Rd
55530755159b148b17ec3035eab1a4c1 *man/mergeBoxplotStats.list.Rd
0d240af23833ebc34bcee67a3db34611 *man/nbrOfArrays.ChromosomalModel.Rd
ac3f9cbcf27e8e0782534e9ee6618d3e *man/nbrOfArrays.Explorer.Rd
bc73b17ca1c45687f75e50a5a42e4644 *man/nbrOfChipTypes.AromaMicroarrayDataSetTuple.Rd
e11b05e2d85aec64ab5006d108b2715d *man/nbrOfChipTypes.ChromosomalModel.Rd
88d60ea907d934931c26755796001f30 *man/plotTracks.PairedPSCNData.Rd
c9340e751d15297bc7320dcfaa444d1d *man/process.AromaTransform.Rd
5417f7cf807fce24ee0c148a1f0c0d99 *man/process.ChromosomeExplorer.Rd
d86acc15ba6712a67876c7ecb20a9579 *man/process.Explorer.Rd
fdf0690d56af95173940f3bab56b553e *man/processTime.Rd
6bd4b4b43b4ac3f225a4f8b3bbc3e65f *man/readFooter.AromaTabularBinaryFile.Rd
c2371bd719738c6236dc5e02c2dce879 *man/segmentByCBS.RawGenomicSignals.Rd
2e579a31a7ac06fa853ce61e2ab92817 *man/segmentByGLAD.RawGenomicSignals.Rd
8ccf2df71dabd088f8a9849b08f0426b *man/segmentByHaarSeg.RawGenomicSignals.Rd
70312d2127636ab7dc23c071b2d715d8 *man/segmentByMPCBS.RawGenomicSignals.Rd
0090af42557f47f04a722762d71c58f6 *man/setAlias.Explorer.Rd
674e68192ad3eb07f24ebb3444391888 *man/setArrays.ChromosomeExplorer.Rd
730bfd4ac108da42a3d9bd58d582de95 *man/setArrays.Explorer.Rd
7dd02776847798bf668f006629db885a *man/updateSetupExplorerFile.ChromosomeExplorer.Rd
5a5dfa4b2a7fd37753befdec1178d42e *man/writeDataFrame.AromaUnitSignalBinaryFile.Rd
b5b16e72e7f3226e759960e36d22e31d *man/writeDataFrame.AromaUnitSignalBinarySet.Rd
5dd111e0cc926be550855cbcb2aa4f93 *man/writeDataFrame.AromaUnitTabularBinaryFile.Rd
026f00f0e96f4ac79fc51b1e2bab5e7b *man/writeFooter.AromaTabularBinaryFile.Rd
9b2db85499f26fbfc2ff6ab333d0af93 *tests/PairedPSCNData,SEG.R
7d32b02db7c00c0ec24694cb14a821a6 *tests/PairedPSCNData.R
b671091978457bf53a2f501e7604afab *tests/RawCopyNumbers,states.R
f21e533c9736818da1333914264e79b9 *tests/RawCopyNumbers.R
638cdcb9d3954ef506e47666bc724057 *tests/RawGenomicSignals.R
5194608cd9aa42ca7aef26fb21d3954d *tests/RawGenomicSignals.SEG,MP.R
10988a7b74be8050bb7ca4478637a2fa *tests/RawGenomicSignals.SEG.R
e4c9e1bc43043f7ecb5517dc2dfb6381 *tests/RichDataFrame.R
def92ce7053b23745e275bfe93e16c3b *tests/SegmentedCopyNumbers.R
47979e8362bcba87b88f493efa73654b *tests/aromaSettings.R
896bf1038b8dbcebcd2139d2f1c694e7 *tests/binScatter.R
d2d562c701931d2856de375618504055 *tests/colBinnedSmoothing.R
366847aeb9be032fb440fc6f164ce54d *tests/colKernelSmoothing.R
05661d58da74cb01d82d37b350884785 *tests/fitGenotypeCone.R
fcbeb60419c29e99d3b37dc14e01a63f *tests/fitMultiDimensionalCone.R
ad0aae8310b99e3b561c271d3864bf7b *tests/matrixBlockPolish.R
22964384e5fa59f71187291156aaf596 *tests/mergeBoxplotStats.R
