f79ad8ac89de2e3284fc5c55b6d215e6 *DESCRIPTION
7c4539503f86f15bd2a819c80ef9e346 *NAMESPACE
3183e4f2da91c06fee75a5ab303b68ae *R/000.R
2a7125edfb8390d0c00a3b4885ceb399 *R/006.fixVarArgs.R
dcb0e44d79e9859ee6006eb8c70b2837 *R/999.NonDocumentedObjects.R
a8420b1b29b708a3a756eb0112b2e5af *R/999.package.R
abd33609f512816f1f1232ee2115707f *R/AbstractCurveNormalization.R
2b5f3ac22c3e7efc277f62988ddb338e *R/C1C2.R
e20d10ca4423327dec7c4ec32cbe564e *R/CBS.findAtomicAberrations.R
bb6ec46bff6bf9750fb0922d5ec5df58 *R/CartesianSnpData.R
e5f35a4cf7286a92f25db659991cd0e8 *R/CopyNumberRegions.findAtomicAberrations.R
02d57703a48958df565ee990dc4e01c2 *R/MultiSourceCopyNumberNormalization.R
caa28c7c68361303fe56e8c4862fb204 *R/MultiSourceCopyNumberNormalization.XTRAS.R
21c30da0242194a67cb905388bd23664 *R/NaiveFracBGenotyping.R
f89d23a5b3eca7190e0589461fb20a4a *R/PairedPSCBS.BOOT.R
088b6818a97ac0ed10b4e23b4845b027 *R/PairedPSCBS.CALL2.R
47addb3a5f6ce9ed22696ec80ed53653 *R/PairedPSCBS.NORM.R
f259538fdaf3c8afa0296393eb62c43b *R/PairedPSCBS.PLOT3.R
2a6aa2d6e98219b63f1b9ae1178f16e3 *R/PairedPSCBS.calibrateC1C2.R
39bb6a3c22ea6001bb4c27df775388da *R/PairedPSCBS.deShearC1C2.R
a4b081b714c62f7e6cf8ee54bd1261a6 *R/PairedPSCBS.findAtomicAberrations.R
4d5e8b5febc25190774aa0e392e38239 *R/PairedPSCBSFile.R
43f2c1fff17dffcad68649be7d34e625 *R/PairedPSCBSFileSet.R
528c50d2cbbbe6ed41fdc368ca49ec3c *R/PairedPscbsCaller.R
6d22d3611899bb58b709b1193c4a4d02 *R/PairedPscbsModel.R
6113f7beb4e6cee610efb40709c7cd3f *R/PeaksAndValleys.EXTS.R
63897a16b173738b7d165a6091411c56 *R/PolarSnpData.R
444bf8d0c5f8224339504e279f27133f *R/PrincipalCurve.XTRAS.R
003d650eceda9f7c7f50eaf705308edb *R/PrincipalCurveNormalization.R
c24e370cdb6101cf6eb5e3a34336ad6f *R/PruneCNA.EXTS.R
f7e44e099bad6a14e1acd8385e87e90d *R/PruneCNA.PLOT.R
8805bc3559c73288476f2d581de21865 *R/RawAlleleBFractions.XTRAS.R
cd2ac6b422133f0bc8f50b152f63edb0 *R/RawGenotypeCalls.R
1a641700c07f3e950e5e96af18da89b9 *R/SnpData.R
a8881b597bf75719d138f669bc4fa6da *R/TotalCnBinnedSmoothing.R
13e0888d4012b6fb0b4bd6bab83152c5 *R/TotalCnKernelSmoothing.R
d99907360c0555441dd6666d0ef26d66 *R/TotalCnSmoothing.R
ff55137c78b4b74f4b80f92109ad481d *R/TotalFracBSnpData.R
daad51a190aa3c21a9d53e77b059c754 *R/TumorBoostNormalization.R
0a043f451f43ad6813c748588bab33d0 *R/XYCurveNormalization.R
313b0861f26d642e6bf0940ad1e58b21 *R/calculatePairedPSCNByGenotype.R
35956dbea48aa53118535f23edbc19c9 *R/callXXorXY.numeric.R
b393416afe0c20be911394f68c049f42 *R/cnr.R
82b5579f57b71ffa0fb06e1caf8c41c6 *R/findCopyNumberNeutralState.R
9d677807da6bab178f916e6b02a650f0 *R/fitLoessKD.matrix.R
cb1f41157d2d72f1887d997a214a0c0f *R/makeSmoothSplinePredict.R
9bda6a1ac439bda0e945dea376595be8 *R/normalizeMirroredBAFsByRegions.R
58c81a554713374f32d1a3ae37ecf915 *R/normalizePrincipalCurve.matrix.R
2f42c2a2fcd396e56800e32979af8f92 *R/principal.curve.pairs2.R
d69f5fd9e14772a960654d3ae332658e *R/pruneCNA.R
adbc0235cbac65555365715ca26becee *R/segmentByPruneCBS.R
127976c87117e8d24c96d85e41a12bf3 *R/testAllelicBalanceByBAFs.R
3d82cd379fd25fbed1a1846a17417c92 *R/testEquality.R
d09c3c692406ff705ffaa5e22509abac *R/zzz.R
999ed8b08d53def9780389d25fb6e64f *incl/999.missingdocs.txt
5135155a71eefccbccfd5d0631e19be9 *incl/BengtssonH_2003.bib.Rdoc
a5802780d34b3ff8437784a76ae78891 *incl/PairedPscbsModel.Rex
14037ef8c12221dab42fe638502c9da8 *incl/TotalCnBinnedSmoothing.Rex
7e590840468c4493ae3dbfb562f0a8e3 *incl/bootstrap.PairedPSCBS.Rex
f375946ae2dd987927538eed6912d32a *incl/calibrateC1C2.PairedPSCBS.Rex
1a228ce5c21e8d152aae219990573eeb *incl/callAllelicBalanceByBAFs.PairedPSCBS.Rex
f8ac3e48929f257115c41f7231ddaf63 *incl/callCopyNeutralRegions.PairedPSCBS.Rex
6a0dcb67c7231409f2f30bdb6d5cc359 *incl/cnr.Rex
f0b535b67c051eda023c34f1d7a0fb05 *incl/deShearC1C2.PairedPSCBS.Rex
1c7a4dfabeed21c6bf4bd8472ae2a663 *incl/findAtomicAberrations.Rex
c07ed58c7fbb3df559956037b4ddbd37 *incl/normalizeBAFsByRegions.PairedPSCBS.Rex
5ead64df77f7a5da88f44a2402a6b22a *incl/orthogonalizeC1C2.PairedPSCBS.Rex
e995a68250e549f43f82713701008c3b *incl/pruneCNA.Rex
274598b3a10ee67aab6d49128dbe97d1 *inst/CITATION
fd82ce28b2c990cb848707d9b35e460f *inst/NEWS
56445dca114fa4f841ff3fcbfbe5edd7 *inst/templates/rsp/PairedPSCBS,deShear,report.tex.rsp
f01bbc88ade170e0dcb4c76fac17fe7d *inst/templates/rsp/bioinformatics-journals-abbr.bib
f3907cf5bef1f44c8c15558e94274a18 *inst/templates/rsp/natbib.bst
f690ef923e880968c45b6debb29ea434 *inst/testScripts/devel/C1C2/21.PairedPSCBS,deShear,report.R
8caf2dafb44f72ba98050c9d0f7c60d7 *inst/testScripts/devel/C1C2/31.PairedPSCBS,DP,deShear.R
f810297ab7440a112afb3bdc43ec5d0f *inst/testScripts/setup/01a.downloadAllAnnotationData.R
5f05ccdf45a5febf8b00eb45e9283ffb *inst/testScripts/setup/01b.downloadAllRawDataSet.R
9654d2efda9ee39dc5ff6550d82f18dc *inst/testScripts/setup/01c.installAllPackages.R
271dfddaddc96369d8adbb5e754afa2a *inst/testScripts/setup/99a.cleanupRootDirectories.R
587b454a0475abb90c181ac01cad519b *inst/testScripts/setup/spawnTests.sh
0ef29c99d7c3ba6106d41a297db530d7 *inst/testScripts/system/CondSegmentation/test20090927,TBN,plot.Rex
09bf83c1e0b71705375b4ce57152c7b7 *inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex
e9a432b7306cb17e24ac48977926d63b *inst/testScripts/system/CopyNumberProfiles/20100909a,findAtomicAberrations.Rex
af6eeccdbb067ebada5832b7f24a883b *inst/testScripts/system/CopyNumberProfiles/20100909b,NormalContamination.Rex
63c081b74fc801964724d0242a39c68f *inst/testScripts/system/CopyNumberProfiles/20100911a,TumorClonality.Rex
4bd04f54c80535e83b86856fe8fa6ea5 *inst/testScripts/system/CopyNumberProfiles/20100911b,TumorClonality,lineage.Rex
d0a1d14e4121abf78de114ecd663041f *inst/testScripts/system/CopyNumberProfiles/20100912a,SegmentationStdError.Rex
d863e583331b3d10c3413d06af21539d *inst/testScripts/system/CopyNumberProfiles/20100912b,Saturation.Rex
ca955d2b1405e8849bebb081e67c3caa *inst/testScripts/system/CurveNormalization,OV/test20090715a,waves.Rex
be60e6457577af5349e3346e4505f93b *inst/testScripts/system/MSLHN/20091218,TCGA,MSLHCN.Rex
753590f4e944f639b8a9e2109e301175 *inst/testScripts/system/MultiPlatform/test20090208,TCGA,MSCN.Rex
776743b5d701792443825fe7dfedbaf5 *inst/testScripts/system/MultiPlatform/test20090209,TCGA,plot.Rex
0b1889427ebbce449b9eccca850587ad *inst/testScripts/system/MultiPlatform/test20090210,TCGA,MSCN,plot.Rex
144ae249c2aa7209cc653594313f3286 *inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,shifts.Rex
1c52de59c6c78c8a6da9a0696bc04fb5 *inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,wCBS.Rex
7aad51dc324e8277edd754fd197dc1e6 *inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,weights.Rex
4e67f71ce6bf8a4c5378e9856a28d4d1 *inst/testScripts/system/MultiPlatform/test20090720,TCGA,MSCN,tracks.Rex
ef33bbc64582d040d7271a23f3bcf414 *inst/testScripts/system/MultiPlatform/test20100102,TCGA,MSCN,mpCBS.Rex
57960543afcf9532e03a9375f437371a *inst/testScripts/system/TumorBoost/test20090429a,NGC.Rex
a67f70ddefe502be88ed003d3913adf8 *inst/testScripts/system/TumorBoost/test20090429b,TBN.Rex
32f4129918232454cafe62afd554dddb *inst/testScripts/system/TumorBoost/test20090429c,TBN,plot.Rex
31f51ad554b5c397ea7c079f24d1d18f *inst/testScripts/system/TumorBoost/test20090429d,TBN,LOH,plot.Rex
9b5171a5b6efb39d1c6aae9b62e74d9f *inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex
3209226df15cd8b6bb27aaa7e383905e *inst/testScripts/system/chipTypes/GenomeWideSNP_6/01a.downloadAnnotationData.R
afc69cbf8bb1abde765bc0e5ff589487 *inst/testScripts/system/chipTypes/GenomeWideSNP_6/01b.downloadRawData.R
dd4cc569e94c9529b92b51a99ef77cfd *inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2,20111026.Rex
290156b8f02f00de6cc2dd651cd9c194 *inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2.PairedPSCBS.Rex
72474da2c45d9fd66af65828399b2611 *inst/testScripts/system/chipTypes/GenomeWideSNP_6/deShearC1C2.PairedPSCBS.Rex
a493230cf30b4c955fc69d1a58fba954 *inst/testScripts/system/chipTypes/GenomeWideSNP_6/normalizeLoess2D.PairedPSCBS.Rex
674117c714550115376c102c2f5f8743 *inst/testScripts/system/chipTypes/GenomeWideSNP_6/orthogonalizeC1C2.PairedPSCBS.Rex
41d961f22c3d9756c325ef366b8dee78 *inst/testScripts/system/ortho/TGCAPairedTotalAndFracBDataTuple.R
198ba52617515636e58790c87c4e9a34 *inst/testScripts/system/ortho/tcga.Rex
084f264472625fedfaca7d88bd40b123 *inst/testScripts/system/ortho/utils.Rex
52ff7f7a40343a46e60741aa9c89ca2f *inst/testScripts/system/pairedPSCN/R/00.setup.R
5d65a929aa2e6160a4f5e19a13370708 *inst/testScripts/system/pairedPSCN/R/getTumorNormalPairs.R
15338d279b07afa255702353955bfd7f *inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R
eae8a4ba1068a1f7e37fd59dc0404c58 *inst/testScripts/system/pairedPSCN/R/zzz.R
f2cc2de4caf80b45454e7139afeba40d *inst/testScripts/system/pairedPSCN/genomicPlots.tex.rsp
6e62c70a93c2c479bbdea25a574c4471 *inst/testScripts/system/segmentation/20091110,CBS.Rex
4837bfe401cf690d9429a35a49dc789f *inst/testScripts/system/tracks/20091008,HCC1143,CRMAv2-dChip-GTC,plot.Rex
9fd3e093be33d76a2694c9ecf40873e4 *inst/testScripts/system/tracks/20091010,TCGA,plot.Rex
f02e385e97eceb7e95013040d151e6cd *inst/testScripts/system/tracks/utils.R
347d646745571a5bf29813aff3e03bef *man/AbstractCurveNormalization.Rd
f70b1ff303a16478d302e5ff5e5788d8 *man/MultiSourceCopyNumberNormalization.Rd
3fec203d77875944914c5a5c48ff3ff9 *man/Non-documented_objects.Rd
066b2c7422ce41b7fa18740b93cc65ce *man/PairedPscbsModel.Rd
4a0cf92a87f64d0014d0b47c8c3109a4 *man/PrincipalCurveNormalization.Rd
6bc0b8799e05e848f9acb23fb94aca74 *man/TotalCnBinnedSmoothing.Rd
bdd899cd2290fc0b8dc0d7a4ca1d17ff *man/TotalCnKernelSmoothing.Rd
3c2204d7042d8507df2171bf3f687c73 *man/TotalCnSmoothing.Rd
824bd178d49e400e9b04f33e46270314 *man/TumorBoostNormalization.Rd
ca57722ee2988f3d9fa935e550a1deb5 *man/XYCurveNormalization.Rd
2939b7a0ad8699bbf31c7f8669009765 *man/aroma.cn-package.Rd
7ef3a45647fa3c7b0a7471b4366b23c3 *man/calibrateC1C2.PairedPSCBS.Rd
2ce9109ab512b6da1e9ddd7bc064da22 *man/callAllelicBalanceByBAFs.PairedPSCBS.Rd
ef32949d2b7f548e20a4e4016c6654fc *man/callCopyNeutralRegions.PairedPSCBS.Rd
2c5aefce7739f716db6e0b1bc316c905 *man/callPeaks.PeaksAndValleys.Rd
35a40f3e931b6872d6a2038892e73df6 *man/callXXorXY.numeric.Rd
f761c6b962f69d93855b10613bed6007 *man/cnr.Rd
4d16d0d07a51afac0ac353f75068fb39 *man/deShearC1C2.PairedPSCBS.Rd
ef10b0268836641766c037cad9e93917 *man/extractTupleOfDataFiles.MultiSourceCopyNumberNormalization.Rd
e9dc5ced5e166340b30421ee9fd6f219 *man/findAtomicAberrations.CopyNumberRegions.Rd
8028f82dde36b0314a49858276a1b8a7 *man/findNeutralCopyNumberState.Rd
c141ae6e7f27938430d1adedefd84738 *man/fitOne.MultiSourceCopyNumberNormalization.Rd
7a7502b2f34461bec685fcdc03b6623f *man/getAllNames.MultiSourceCopyNumberNormalization.Rd
841df1990d8ca013fa84599704d45c85 *man/getFitAromaUgpFile.MultiSourceCopyNumberNormalization.Rd
2c8e757d54f5686922eb1f0d65277436 *man/getInputDataSets.MultiSourceCopyNumberNormalization.Rd
7b8f77d7c0e4b5a6024e15af9c6e9d4f *man/getSmoothedDataSets.MultiSourceCopyNumberNormalization.Rd
a9c1f99e5e96b0c67b570076325b7e2b *man/getSubsetToFit.MultiSourceCopyNumberNormalization.Rd
0f5f41272443041898f9a138c373451c *man/normalizeBAFsByRegions.PairedPSCBS.Rd
112d603ff11026f9c4d48333c6f3c4b4 *man/normalizeMirroredBAFsByRegions.matrix.Rd
b0e220fa44509f3f2a0d30aeb2de1352 *man/normalizePrincipalCurve.matrix.Rd
fc9c2fc14d41f9143daf25040317c809 *man/process.MultiSourceCopyNumberNormalization.Rd
6023f4b309d16102bdd253623de9bab6 *man/testAllelicBalanceByBAFs.Rd
