8c66ddd97a510a5d8bc6b11ef26e653c *DESCRIPTION
41adf03c03852bc0cdb10c20c53ce625 *NAMESPACE
81ff8360396bae44b9cd496e175f4d60 *NEWS
4bcbb5139128447d6309d89980703e1c *R/000.R
2a7125edfb8390d0c00a3b4885ceb399 *R/006.fixVarArgs.R
f5e112bbebf8845bc02bf820be42c94b *R/009.setup.R
8c84ae7dfcdb4bbf0b4b7fee2e933964 *R/021.dynamic_imports.R
ae5c7a6c9cd6ac16c5192b8acb930e5d *R/999.NonDocumentedObjects.R
400bcd85834705f8d73e49563d1fc3e0 *R/999.package.R
9a061407160e5244f7c301ece89d50cb *R/AbstractCurveNormalization.R
cf98576d2bce9db3d4678c23c9cef0b9 *R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R
bb0d57c1d2a7c2ccd9699a5d5593091a *R/C1C2.R
0281e310f438c4774cd0b696cc68b2f5 *R/CBS.findAtomicAberrations.R
bb6ec46bff6bf9750fb0922d5ec5df58 *R/CartesianSnpData.R
f1112f985bc222d6599d2cff0c325848 *R/CopyNumberRegions.findAtomicAberrations.R
aa69819ca1922481e53850c96f3a8dfd *R/MultiSourceCopyNumberNormalization.R
caa28c7c68361303fe56e8c4862fb204 *R/MultiSourceCopyNumberNormalization.XTRAS.R
6142fa615b87dc4cd9d4fa6757c0a710 *R/NaiveFracBGenotyping.R
09ad5ce56ddb483e5c87b25fda813e0a *R/PairedPSCBS.BOOT.R
3809598afcb9f92797ba8d72cde42205 *R/PairedPSCBS.CALL2.R
fc7565eed0355e760991c4defe8c5b80 *R/PairedPSCBS.NORM.R
aca563243c50b583d2c20b1888c075be *R/PairedPSCBS.PLOT3.R
c9cdd6d3b95e240bdf2ae4df96730094 *R/PairedPSCBS.backgroundCorrect.R
a7a0d70559713bb2eef01c0e9135d0e8 *R/PairedPSCBS.findAtomicAberrations.R
3bb79257400bf717d53fe3052af21267 *R/PairedPSCBS.fitC1C2Peaks.R
4d5e8b5febc25190774aa0e392e38239 *R/PairedPSCBSFile.R
8fb599dddd637675781acf768d0c2e6d *R/PairedPSCBSFileSet.R
e1704c50c57b127308ea06341d0d9acf *R/PairedPscbsCaller.R
699666b2bc6110f28e4a7ed362b4b099 *R/PairedPscbsModel.R
fb623c38fe465e972f283096ee4eb528 *R/PeaksAndValleys.EXTS.R
63897a16b173738b7d165a6091411c56 *R/PolarSnpData.R
d70692312ef847a42347ff3dcec764ff *R/PrincipalCurve.XTRAS.R
e3063c7054f31a2b8dddef5e6657261d *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
9132e95db6f92eea63e29172fe23a929 *R/TotalCnBinnedSmoothing.R
ee359e1828300795552940d11de919b2 *R/TotalCnKernelSmoothing.R
002a1631ea7ef14a6a2321acba8a792f *R/TotalCnSmoothing.R
80c73f90d5cc53d98bcd5eb97d47b871 *R/TotalFracBSnpData.R
c94e71a94ce4a46d00658e4b72f5f013 *R/TumorBoostNormalization.R
e3bec187dc449036ee2c1b601f6cfb63 *R/XYCurveNormalization.R
313b0861f26d642e6bf0940ad1e58b21 *R/calculatePairedPSCNByGenotype.R
417cdb43a4e6e625d36bbb2257bc0d14 *R/callXXorXY.numeric.R
ba2ef61823b3974150ce01c005773c49 *R/cnr.R
9d677807da6bab178f916e6b02a650f0 *R/fitLoessKD.matrix.R
d53bdac1521b3ec26e755db0996a9a0c *R/makeSmoothSplinePredict.DEPRECATED.R
d47c4eb15c1d027d1a79d1f41e481a10 *R/normalizeMirroredBAFsByRegions.R
b547be1a863227d5347bedc0fcd4c502 *R/normalizePrincipalCurve.matrix.R
053c1fdf4c85c1207b91ced7136f5152 *R/principal.curve.pairs2.R
f5ef50ff7117dc0a34d342268aaa8eb7 *R/pruneCNA.R
02b3fd8775ac289694b17bd3da9efa6d *R/segmentByPruneCBS.R
0ff9fab55cc2f6b51fbf7afbeb1d23de *R/testAllelicBalanceByBAFs.R
3d82cd379fd25fbed1a1846a17417c92 *R/testEquality.R
75ad3c853c55fd01c0a5278146057ca2 *R/zzz.R
acebc237c52e1b8dc71fd6622cc75444 *inst/CITATION
c1c1b071c902ad6ab220f79a3178888c *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
0618e2db8237982057da9cf4fbeaf2fb *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
93a1d82c25edb670e5905cd01cb7403a *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
81270117561989d22eb5450574e99694 *inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex
dd4cc569e94c9529b92b51a99ef77cfd *inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2,20111026.Rex
290156b8f02f00de6cc2dd651cd9c194 *inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2.PairedPSCBS.Rex
5bca8b5b48b0763455917047ca5e38b2 *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
63b25bfcba3550e2df64a0ef3528449e *inst/testScripts/system/pairedPSCN/R/00.setup.R
c11627802fe64d57a0d320b2fd322529 *inst/testScripts/system/pairedPSCN/R/getTumorNormalPairs.R
84f679b47dee01c4730af524b702c1fb *inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R
8886c91c0fd41c00562723fd5a41a345 *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
103167d9ef113e7906cc2120102048ef *man/AbstractCurveNormalization.Rd
c0024478884028a0f83af664f3292787 *man/MultiSourceCopyNumberNormalization.Rd
c05d91010c6630d181fc09b069e0ee87 *man/Non-documented_objects.Rd
9038c63373813f71f36bbdf6ccf90088 *man/PairedPscbsModel.Rd
0c1697fefe3943bdcedcb61aabca6635 *man/PrincipalCurveNormalization.Rd
4d0e930cc1c55c79882351886a0a2d87 *man/TotalCnBinnedSmoothing.Rd
0c4d7e7dd5bc8852462a4a833b581b01 *man/TotalCnKernelSmoothing.Rd
29498a02126f42c7b06ecd53cf5e630e *man/TotalCnSmoothing.Rd
aab82720685fc0789d99117c213e3577 *man/TumorBoostNormalization.Rd
8809168ad7d356571fe036e205f19a86 *man/XYCurveNormalization.Rd
dace5b457aa6d0495a45108b7d87ee8b *man/aroma.cn-package.Rd
c099fd26c6e71dc1fca4f8433140ef5c *man/callAllelicBalanceByBAFs.PairedPSCBS.Rd
5713485b871d7abcf035406d4f832b51 *man/callCopyNeutralRegions.PairedPSCBS.Rd
93c5264f4800495367f70ca09526d491 *man/callPeaks.PeaksAndValleys.Rd
90e08b10b336d321db225552ba1d1a60 *man/callXXorXY.numeric.Rd
be2469e7fd2ad0f23ac556e3862872e2 *man/cnr.Rd
84ef9efe4c955fa964c432f027854e94 *man/extractTupleOfDataFiles.MultiSourceCopyNumberNormalization.Rd
51c313c2f3a57c31f9e65e3eca7e9cc0 *man/findAtomicAberrations.CopyNumberRegions.Rd
210f7d31dc6f9f9d7b357941c700b951 *man/fitOne.MultiSourceCopyNumberNormalization.Rd
4200854acc17cc519d90fd670612cfa4 *man/getAllNames.MultiSourceCopyNumberNormalization.Rd
68fb85563fb60b511bee95da8e13ccfb *man/getFitAromaUgpFile.MultiSourceCopyNumberNormalization.Rd
4e42700e5778314bac38f3efc3a48a0f *man/getInputDataSets.MultiSourceCopyNumberNormalization.Rd
36944d175ee21ffc5948df92db4e8df1 *man/getSmoothedDataSets.MultiSourceCopyNumberNormalization.Rd
295d9c7ed39d342933b701a2d1839856 *man/getSubsetToFit.MultiSourceCopyNumberNormalization.Rd
00eca193885fb6776126253daa760966 *man/normalizeBAFsByRegions.PairedPSCBS.Rd
9c0b893829ecaabace1e787bf268e93d *man/normalizeMirroredBAFsByRegions.matrix.Rd
532068d8070c92311f62d896d81da354 *man/normalizePrincipalCurve.matrix.Rd
935bf1cff7b670a8bbe4248883471a34 *man/process.MultiSourceCopyNumberNormalization.Rd
463c05c1a00c0dfb32826fb28f45cd3c *man/testAllelicBalanceByBAFs.Rd
51808a42e3b15841ee2127c8427e373c *tests/callAllelicBalanceByBAFs.PairedPSCBS.R
75e63fec8c517d7dd2604ebfe13db2a9 *tests/cnr.R
