843f3075606dbff65920fe22ab6cbfa5 *DESCRIPTION
cfcd6dc96da77c0ace0d61c5b3dda123 *NAMESPACE
3183e4f2da91c06fee75a5ab303b68ae *R/000.R
2a7125edfb8390d0c00a3b4885ceb399 *R/006.fixVarArgs.R
ae5c7a6c9cd6ac16c5192b8acb930e5d *R/999.NonDocumentedObjects.R
573bd0d38eeb3cc44bcd0e3872336076 *R/999.package.R
a0dcf2956afa8fc296c2dbd388f5b495 *R/AbstractCurveNormalization.R
2b5f3ac22c3e7efc277f62988ddb338e *R/C1C2.R
33de613b7c4e5fb6371e315c234ac2d7 *R/CBS.findAtomicAberrations.R
bb6ec46bff6bf9750fb0922d5ec5df58 *R/CartesianSnpData.R
3a6c8e07e122cddb9c2ee1a9bb7fe344 *R/CopyNumberRegions.findAtomicAberrations.R
f4cc453522bfa62f88683609a9353aec *R/MultiSourceCopyNumberNormalization.R
caa28c7c68361303fe56e8c4862fb204 *R/MultiSourceCopyNumberNormalization.XTRAS.R
21c30da0242194a67cb905388bd23664 *R/NaiveFracBGenotyping.R
09ad5ce56ddb483e5c87b25fda813e0a *R/PairedPSCBS.BOOT.R
4c9bb71a7f33a1bb115e107cb20db10f *R/PairedPSCBS.CALL2.R
c352b0cc47987d5e3c0ccc27c5d4b1e6 *R/PairedPSCBS.NORM.R
f259538fdaf3c8afa0296393eb62c43b *R/PairedPSCBS.PLOT3.R
bbb46d8c7122929306bf2c6b32c69f53 *R/PairedPSCBS.calibrateC1C2.R
5e0dc33239c2b637170e76b260e5992b *R/PairedPSCBS.deShearC1C2.R
60e4dcd26b9589f07b559bd3b90a9946 *R/PairedPSCBS.findAtomicAberrations.R
4d5e8b5febc25190774aa0e392e38239 *R/PairedPSCBSFile.R
43f2c1fff17dffcad68649be7d34e625 *R/PairedPSCBSFileSet.R
528c50d2cbbbe6ed41fdc368ca49ec3c *R/PairedPscbsCaller.R
6d22d3611899bb58b709b1193c4a4d02 *R/PairedPscbsModel.R
eb4b45992c7acd899137aa7dbefeef8f *R/PeaksAndValleys.EXTS.R
63897a16b173738b7d165a6091411c56 *R/PolarSnpData.R
444bf8d0c5f8224339504e279f27133f *R/PrincipalCurve.XTRAS.R
e6676ec82e3463669282e6867717e23f *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
acd119428d382c19937e9f926f67a3b5 *R/TotalCnSmoothing.R
ff55137c78b4b74f4b80f92109ad481d *R/TotalFracBSnpData.R
bae1f91a2e5ef0fa81004ca8f1b521f0 *R/TumorBoostNormalization.R
0d9e23c9261a158c4adc6dc4c5260d25 *R/XYCurveNormalization.R
313b0861f26d642e6bf0940ad1e58b21 *R/calculatePairedPSCNByGenotype.R
42d24993b49bb135ff20e8e8f712ffd5 *R/callXXorXY.numeric.R
ba2ef61823b3974150ce01c005773c49 *R/cnr.R
9d677807da6bab178f916e6b02a650f0 *R/fitLoessKD.matrix.R
546edcd021fd0fff839967533f6ba379 *R/makeSmoothSplinePredict.DEPRECATED.R
1b1870a071bcf4f47586250237668a6b *R/normalizeMirroredBAFsByRegions.R
b629fe81255bb82b1ddfd4052e81d47d *R/normalizePrincipalCurve.matrix.R
2f42c2a2fcd396e56800e32979af8f92 *R/principal.curve.pairs2.R
f5ef50ff7117dc0a34d342268aaa8eb7 *R/pruneCNA.R
adbc0235cbac65555365715ca26becee *R/segmentByPruneCBS.R
85ddeb0340c7cdb6ec9748292ca4c492 *R/testAllelicBalanceByBAFs.R
3d82cd379fd25fbed1a1846a17417c92 *R/testEquality.R
e3014d32d6e7ebee7207fba4d28d4062 *R/zzz.R
274598b3a10ee67aab6d49128dbe97d1 *inst/CITATION
75a574dded25d6b7eff05043bf6b3021 *inst/NEWS
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
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
ac388d032d702f50aba63f1ccbe28f33 *man/AbstractCurveNormalization.Rd
d09ac150934dc31f84d67def6c20db9c *man/MultiSourceCopyNumberNormalization.Rd
42f6351b294503f1323f9a98392fc26b *man/Non-documented_objects.Rd
0a976d94efcefa3e18f4e5ea03926cd9 *man/PairedPscbsModel.Rd
abefee921d4d25514d24c6acf2376f1d *man/PrincipalCurveNormalization.Rd
656e6360995a77293cbfeac2ad9dbfde *man/TotalCnBinnedSmoothing.Rd
71106fbe70314364ca05ad7140c15c1d *man/TotalCnKernelSmoothing.Rd
32b965a6110495f1395b1ee7c20c1e89 *man/TotalCnSmoothing.Rd
3fba1fe9aa3e716ba4e577eae861820a *man/TumorBoostNormalization.Rd
58d4a07fb98b505124044a10490f974a *man/XYCurveNormalization.Rd
bdcf2a302202308aeec9ba4afe4bd17f *man/aroma.cn-package.Rd
391f1215d44d7e15cfa52bb4175fe802 *man/calibrateC1C2.PairedPSCBS.Rd
3fd5eabcd293bb1e5c5c0815d4560d06 *man/callAllelicBalanceByBAFs.PairedPSCBS.Rd
5713485b871d7abcf035406d4f832b51 *man/callCopyNeutralRegions.PairedPSCBS.Rd
1fe078dad949a9d7b4257fc73f8a0635 *man/callPeaks.PeaksAndValleys.Rd
d6888d6b57fed99937be3defa4e32d1e *man/callXXorXY.numeric.Rd
be2469e7fd2ad0f23ac556e3862872e2 *man/cnr.Rd
36d4dabb30fc8a590211b1daceb4da9f *man/deShearC1C2.PairedPSCBS.Rd
84ef9efe4c955fa964c432f027854e94 *man/extractTupleOfDataFiles.MultiSourceCopyNumberNormalization.Rd
b364bce1a22ea101c897dcbda01ef213 *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
be6484fcd0ebc7fe499a16769c7b4287 *man/normalizeBAFsByRegions.PairedPSCBS.Rd
9c0b893829ecaabace1e787bf268e93d *man/normalizeMirroredBAFsByRegions.matrix.Rd
532068d8070c92311f62d896d81da354 *man/normalizePrincipalCurve.matrix.Rd
935bf1cff7b670a8bbe4248883471a34 *man/process.MultiSourceCopyNumberNormalization.Rd
463c05c1a00c0dfb32826fb28f45cd3c *man/testAllelicBalanceByBAFs.Rd
