25923b0f6ce4edc8c7e31356c7998573 *DESCRIPTION
a0542c2bb6cbd2b120d412589b7a3b6c *NAMESPACE
121bdd18a664b427829430e82a3dcf04 *NEWS.md
694f1ab0fbb4bb254cc3b594c0999b7a *R/000.R
1df04dc13e5ad8dbc137a07bad5a1af1 *R/006.fixVarArgs.R
07d06fd2bb4a10488375ab942d5f5592 *R/009.setup.R
6506e1debb11db91cb1a5501561c7647 *R/021.dynamic_imports.R
411196433a5618d1a8096197d6f9dbe0 *R/999.DEPRECATED.R
dcd82fd492e09e87908164709054a4d3 *R/999.NonDocumentedObjects.R
400bcd85834705f8d73e49563d1fc3e0 *R/999.package.R
b6ea2a71c349ebb08ea1dbdfc1d8d4e4 *R/AbstractCurveNormalization.R
2f1d12155b0f5b49a1a1ecff2f0af7a8 *R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R
05048caa80e19bbffe87503645ff5163 *R/C1C2.R
23aad02bb5a7ff3cd0365210ee1eb3bf *R/CBS.findAtomicAberrations.R
cea29e3e9f7559cde5e061addf2d0598 *R/CartesianSnpData.R
f15a8b3ea3e4d31ef14f9d4c19b8788b *R/CopyNumberRegions.findAtomicAberrations.R
0f6a3411001ae53856c0103776167844 *R/MultiSourceCopyNumberNormalization.R
574feb4e09da0030758fe730c978194c *R/MultiSourceCopyNumberNormalization.XTRAS.R
29fcff7adff0cb58868c6d32b26e996a *R/NaiveFracBGenotyping.R
91acc5ac0c75de182920418c4bf28b22 *R/PairedPSCBS.BOOT.R
4bdd98123bd83b680c6e24d13b001b90 *R/PairedPSCBS.CALL2.R
4ffd4e5b4acc34f9ab9b6032c9288cbf *R/PairedPSCBS.NORM.R
938f86f459b94977be5dfedb3f06dd2c *R/PairedPSCBS.PLOT3.R
54fa9ac41725db8fc2b258027b6285be *R/PairedPSCBS.backgroundCorrect.R
3f7ba1e9440950dab81aeceef8e7c9cb *R/PairedPSCBS.findAtomicAberrations.R
e54f8b85ba6c9abc4760f6c0e5d3379f *R/PairedPSCBS.fitC1C2Peaks.R
6d81c3245db5dfe04ff9490250154f2f *R/PairedPSCBSFile.R
ebb331ac417f32da443bf8b0b5165d26 *R/PairedPSCBSFileSet.R
954e4783cc893184a4064f5ed824a434 *R/PairedPscbsCaller.R
fb5fe00ff8d2077cef4fdc0903c5062b *R/PairedPscbsModel.R
e0dfc8765a5a9a7dd6d9d249b243d808 *R/PeaksAndValleys.EXTS.R
44aa0304a31783d8a2acd21a71e71e9d *R/PolarSnpData.R
a2bdbb16887f4068192ba71a39f14689 *R/PrincipalCurve.XTRAS.R
e3c706f40e60b1f4cf575abacc6d384a *R/PrincipalCurveNormalization.R
6735eb0ceeadaffb4f0dec69e5dd585d *R/PruneCNA.EXTS.R
f42c3d9d6efadafa64f703d0f7824a11 *R/PruneCNA.PLOT.R
eb85bd1cf3b0b5ef1761bce6498320e5 *R/RawAlleleBFractions.XTRAS.R
24488f941fd980ffb0a4f97a166284c2 *R/RawGenotypeCalls.R
46b944557490d9fe17a0f977124faf67 *R/SnpData.R
3d18263783c9dbbbcae924bd90f71297 *R/TotalCnBinnedSmoothing.R
c42002c7994ea985f8b7e04e8036b06b *R/TotalCnKernelSmoothing.R
5530be3b9d065c6347df61aea88e9303 *R/TotalCnSmoothing.R
e050bfec150cc6c04ecb2b4edda165da *R/TotalFracBSnpData.R
8b28a027606750a2de43e2c7d32e7d8e *R/TumorBoostNormalization.R
321b8304200f842c0c3783d443813489 *R/XYCurveNormalization.R
3c55fc3b4d6f331e22167096fa84d5d7 *R/calculatePairedPSCNByGenotype.R
7b467bc4e9c2c7715bcabb0b230cd0eb *R/callXXorXY.numeric.R
7429cec1a121811e1f2c665f64620a67 *R/cnr.R
2ef1d611792cb88980176495cc3f11c1 *R/fitLoessKD.matrix.R
91abdc36af3a7ea83d104ecf378b03cf *R/normalizeMirroredBAFsByRegions.R
e7ba40b33d05c0efe387ed74a6b4e9fe *R/normalizePrincipalCurve.matrix.R
30bec3561b3fd380b5c7c2b5ef978ff9 *R/principal.curve.pairs2.R
20ab8be533e53e4ca5e2ba3139e93f9f *R/pruneCNA.R
fb0f7922af34aaca8316e14d7046bbef *R/segmentByPruneCBS.R
ea5aac0ce98c58c5f5fbaaba6297f776 *R/testAllelicBalanceByBAFs.R
fcdee93bdc8d66b63dd5b11591d294e8 *R/testEquality.R
5d70959a9e051a5666c0524ad97022d9 *R/utils.R
b9dfb7cd7652916d5153f73d884abec4 *R/zzz.R
044d39105d81890b3867281fa191640e *inst/CITATION
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f01bbc88ade170e0dcb4c76fac17fe7d *inst/templates/rsp/bioinformatics-journals-abbr.bib
f3907cf5bef1f44c8c15558e94274a18 *inst/templates/rsp/natbib.bst
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b18b3a27fff4fdd80b6ed813d191e735 *inst/testScripts/devel/C1C2/31.PairedPSCBS,DP,deShear.R
de98567b2f6aec673aa1bb361eabfa26 *inst/testScripts/setup/01a.downloadAllAnnotationData.R
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c9d6599df89939890d79d4e0fc3a79ad *inst/testScripts/setup/01c.installAllPackages.R
64357076edc0e16a42ca5156a8f30b44 *inst/testScripts/setup/99a.cleanupRootDirectories.R
587b454a0475abb90c181ac01cad519b *inst/testScripts/setup/spawnTests.sh
8062b36bdc644134bce65f6cfe74c166 *inst/testScripts/system/CondSegmentation/test20090927,TBN,plot.Rex
1784cbfcf2d30acedbbe9e5b6b9110ec *inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex
0000433b32557bbe0df5931f2dc327cf *inst/testScripts/system/CopyNumberProfiles/20100909a,findAtomicAberrations.Rex
5ceca790b1c5d64857ce036aa641d2c4 *inst/testScripts/system/CopyNumberProfiles/20100909b,NormalContamination.Rex
88c13f733dceabfd4034f68f1affb80d *inst/testScripts/system/CopyNumberProfiles/20100911a,TumorClonality.Rex
21292aa1b85768708c514ebdd0662893 *inst/testScripts/system/CopyNumberProfiles/20100911b,TumorClonality,lineage.Rex
d6f631124870e5ca7329222929346c4d *inst/testScripts/system/CopyNumberProfiles/20100912a,SegmentationStdError.Rex
bed3fb7ffcd1e9ecbcc8394549372310 *inst/testScripts/system/CopyNumberProfiles/20100912b,Saturation.Rex
ca955d2b1405e8849bebb081e67c3caa *inst/testScripts/system/CurveNormalization,OV/test20090715a,waves.Rex
cc84822d533c0c00e5160fe3fcf26b32 *inst/testScripts/system/MSLHN/20091218,TCGA,MSLHCN.Rex
753590f4e944f639b8a9e2109e301175 *inst/testScripts/system/MultiPlatform/test20090208,TCGA,MSCN.Rex
8ee56c3fe6813dce91880ae6afdc47ab *inst/testScripts/system/MultiPlatform/test20090209,TCGA,plot.Rex
8ad8697bfbbcaa9da7bd18b98c923a22 *inst/testScripts/system/MultiPlatform/test20090210,TCGA,MSCN,plot.Rex
3f13b99b3603bdff2614b546365bfa38 *inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,shifts.Rex
d7c8fa6b9cec6c48b5ab8e04eadb75d7 *inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,wCBS.Rex
3df219c76e242e7ad13b5ec5385f4521 *inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,weights.Rex
4e67f71ce6bf8a4c5378e9856a28d4d1 *inst/testScripts/system/MultiPlatform/test20090720,TCGA,MSCN,tracks.Rex
811f60619feb726e279db5eabc06d969 *inst/testScripts/system/MultiPlatform/test20100102,TCGA,MSCN,mpCBS.Rex
dc97b1b3e69e8fd33f7979a94ac31499 *inst/testScripts/system/TumorBoost/test20090429a,NGC.Rex
a67f70ddefe502be88ed003d3913adf8 *inst/testScripts/system/TumorBoost/test20090429b,TBN.Rex
32f4129918232454cafe62afd554dddb *inst/testScripts/system/TumorBoost/test20090429c,TBN,plot.Rex
5060810e7f02288f5bbb43912b45a476 *inst/testScripts/system/TumorBoost/test20090429d,TBN,LOH,plot.Rex
272932638c67aa701782934ee4add363 *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
77fd1f08fa7968d5b3d9f379ea364b64 *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
9f461f221316e63b592c82119a4dad0d *inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R
8886c91c0fd41c00562723fd5a41a345 *inst/testScripts/system/pairedPSCN/R/zzz.R
07a16a200cb5e7af3d5ffbc2b9b1ec92 *inst/testScripts/system/pairedPSCN/genomicPlots.tex.rsp
4568b3a5ef69546d139ad61fd7873b6b *inst/testScripts/system/segmentation/20091110,CBS.Rex
4837bfe401cf690d9429a35a49dc789f *inst/testScripts/system/tracks/20091008,HCC1143,CRMAv2-dChip-GTC,plot.Rex
2ab2f3dfc2cdfc447ed126a5402c62f0 *inst/testScripts/system/tracks/20091010,TCGA,plot.Rex
5bdb756f59634b5954e24d663360a32f *inst/testScripts/system/tracks/utils.R
8c94f300c6ab3e4ee13b6032a5301cb7 *man/AbstractCurveNormalization.Rd
ac489ec8f54bc2cb76bddc889542af50 *man/MultiSourceCopyNumberNormalization.Rd
c05d91010c6630d181fc09b069e0ee87 *man/Non-documented_objects.Rd
05360f51808b071fc2da462bad97853b *man/PairedPscbsModel.Rd
d952f2f328170643b9604907469bcadd *man/PrincipalCurveNormalization.Rd
77dcff6a0b9f7c04210111477b184164 *man/TotalCnBinnedSmoothing.Rd
8e9391425bad62156c776c24108f5629 *man/TotalCnKernelSmoothing.Rd
e41a6bcbe83455e13ffe70db3b7cca0f *man/TotalCnSmoothing.Rd
f65cb43ed875aa1500b4c4ae166336db *man/TumorBoostNormalization.Rd
a883e2b438327c218edda1b24c9cae61 *man/XYCurveNormalization.Rd
0abbc3f0351093eea7742489559c9d1a *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
44cebb52dab60af465ab6957e675156a *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
