9faaa4555801177f085c11ec42394147 *DESCRIPTION
8b1ecca81c7b61b2307ec62aac27b74a *NAMESPACE
3183e4f2da91c06fee75a5ab303b68ae *R/000.R
2a7125edfb8390d0c00a3b4885ceb399 *R/006.fixVarArgs.R
dcb0e44d79e9859ee6006eb8c70b2837 *R/999.NonDocumentedObjects.R
a8420b1b29b708a3a756eb0112b2e5af *R/999.package.R
66a9d02fb87eaa50c54d91d615ea61f6 *R/AbstractCurveNormalization.R
f8c5eb796b88eedea2db358ca05f39bf *R/C1C2.R
183ea527ed7198c4b376144e78d4af2a *R/CartesianSnpData.R
e5f35a4cf7286a92f25db659991cd0e8 *R/CopyNumberRegions.findAtomicAberrations.R
29e4c8422d274282ffa186d828c8502f *R/MultiSourceCopyNumberNormalization.R
4ae6524dd6e9416c9f6bb2383c20abf2 *R/MultiSourceCopyNumberNormalization.XTRAS.R
d85219e85e57c20c7a191ed062ad4649 *R/NaiveFracBGenotyping.R
f183feff738f7cf56857ec17094aadef *R/PairedPSCBS.BOOT.R
656dda1d3f0235405dcb3b6384b80a63 *R/PairedPSCBS.EXTS2.R
8806c711bde94f12cdd5f9b62be0ff42 *R/PairedPSCBS.NORM.R
3783766aacaa1130a97ecc8fc1a73078 *R/PairedPSCBS.calibrateC1C2.R
7308321f00229fc5b92da9f142bc3483 *R/PairedPSCBS.deShearC1C2.R
6681eafb59ac7e06485761956b37d3f8 *R/PairedPSCBS.findAtomicAberrations.R
c982e8e432e1f8a50aef209f20ddc84d *R/PairedPSCBSFile.R
28932a0a68a1e433fd661126065fa9d3 *R/PairedPSCBSFileSet.R
9b65d4132336c099de8944408556220f *R/PeaksAndValleys.EXTS.R
1d7b6cbb445b6f861fc44737bb2812a0 *R/PolarSnpData.R
7488fd881b9949423d500fc825a792cb *R/PrincipalCurve.XTRAS.R
666dfea1582a672dadec6e22e895bf6f *R/PrincipalCurveNormalization.R
4e49d0478141bc9d9f3394aa12592d4d *R/PruneCNA.PLOT.R
8805bc3559c73288476f2d581de21865 *R/RawAlleleBFractions.XTRAS.R
cd2ac6b422133f0bc8f50b152f63edb0 *R/RawGenotypeCalls.R
68f3f8eacbea0b7def02fa35ec7d123b *R/SnpData.R
509d33469f23a0c8400240db8085ca84 *R/TotalCnKernelSmoothing.R
6d2ace346980f129ef048d18d131c08d *R/TotalCnSmoothing.R
7a02b9f5e2b34125752e258291578f03 *R/TotalFracBSnpData.R
6ce08bacdda35eb259464fdae1dd89a3 *R/TumorBoostNormalization.R
0a043f451f43ad6813c748588bab33d0 *R/XYCurveNormalization.R
9042dbc4030bdb983304e38125fcda4e *R/callXXorXY.numeric.R
b393416afe0c20be911394f68c049f42 *R/cnr.R
6024d4a93ea2f7165bc659cc99930732 *R/findCopyNumberNeutralState.R
c2b560cd80b43bda535f23cbb6f16914 *R/fitLoessKD.matrix.R
cb1f41157d2d72f1887d997a214a0c0f *R/makeSmoothSplinePredict.R
8e2da2b9ff81ae14b3d187ed84221db2 *R/normalizeMirroredBAFsByRegions.R
2c0b3444fbc90164524418f5e22a5bc0 *R/normalizePrincipalCurve.matrix.R
2f42c2a2fcd396e56800e32979af8f92 *R/principal.curve.pairs2.R
5cb431160512b8a4765399b5673da0fb *R/pruneCNA.R
016567f1f509e2a5cc91b0b67f2db216 *R/segmentByPruneCBS.R
4446a0f470e9ef961bce6e61d8be76f9 *R/testAllelicBalanceByBAFs.R
06edd68a79f64fb3af5d6a81a742f3f2 *R/testEquality.R
d09c3c692406ff705ffaa5e22509abac *R/zzz.R
365690f557bb2c5b66de7ba491f81271 *incl/999.missingdocs.txt
5135155a71eefccbccfd5d0631e19be9 *incl/BengtssonH_2003.bib.Rdoc
2bdef50dd3e8c8caad97a93b70c3ec64 *incl/bootstrap.PairedPSCBS.Rex
7673963d5340ae58373a0738fc8247b4 *incl/calibrateC1C2.PairedPSCBS.Rex
861a5bc97feb0b34ad1406a42a189c70 *incl/callAllelicBalanceByBAFs.PairedPSCBS.Rex
db8db96e3660c5511e3cf457d2276b9c *incl/callCopyNeutralRegions.PairedPSCBS.Rex
6a0dcb67c7231409f2f30bdb6d5cc359 *incl/cnr.Rex
b41adf49f107eca5d3460515ae7d5677 *incl/deShearC1C2.PairedPSCBS.Rex
1c7a4dfabeed21c6bf4bd8472ae2a663 *incl/findAtomicAberrations.Rex
5782a07f5f86b56ef3e315c5aed3ae53 *incl/normalizeBAFsByRegions.PairedPSCBS.Rex
40e722acaa2d08eabc66f7a0d947a9e8 *incl/orthogonalizeC1C2.PairedPSCBS.Rex
274598b3a10ee67aab6d49128dbe97d1 *inst/CITATION
4526f0bb515bc59ae59e99eea80277b4 *inst/NEWS
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
41d961f22c3d9756c325ef366b8dee78 *inst/testScripts/system/ortho/TGCAPairedTotalAndFracBDataTuple.R
fd78b2bc7be69f75d396351f2ca54f78 *inst/testScripts/system/ortho/calibrateC1C2,20111026.Rex
cb5dbdf36a523c580b459b7d38ee7f84 *inst/testScripts/system/ortho/calibrateC1C2.PairedPSCBS.Rex
72474da2c45d9fd66af65828399b2611 *inst/testScripts/system/ortho/deShearC1C2.PairedPSCBS.Rex
a493230cf30b4c955fc69d1a58fba954 *inst/testScripts/system/ortho/normalizeLoess2D.PairedPSCBS.Rex
674117c714550115376c102c2f5f8743 *inst/testScripts/system/ortho/orthogonalizeC1C2.PairedPSCBS.Rex
3303a8c8a19cf131040afab903ea1c0f *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
2c3f7cee2418a2c7bfec061c83fa1ad6 *man/AbstractCurveNormalization.Rd
11b0b2009dd1e2d6082f9ac6f200d664 *man/MultiSourceCopyNumberNormalization.Rd
9d5df54c701134f3690fdb857d7fd49d *man/Non-documented_objects.Rd
a25064a319d0c256f931a51dd37d5d7d *man/PrincipalCurveNormalization.Rd
6f68bf0d38755f865d6619e38a4daf16 *man/TotalCnKernelSmoothing.Rd
d24464dcb3a567080e69ed210dc7d9f2 *man/TotalCnSmoothing.Rd
aa07515df0315c59310f081b580f40c8 *man/TumorBoostNormalization.Rd
3b9eaa5b3bf74cff1b8ae1f0831ec273 *man/XYCurveNormalization.Rd
0ddb9a7b5629ae0cc52d698d75ee40f8 *man/aroma.cn-package.Rd
a851681b88af088cbac80c6553a9dcd3 *man/calibrateC1C2.PairedPSCBS.Rd
c2bb9ad369ff5b83260c23a915402d8f *man/callAllelicBalanceByBAFs.PairedPSCBS.Rd
ac23c8d10fbbc0994c2772c142c4be8f *man/callCopyNeutralRegions.PairedPSCBS.Rd
e14f9fac62cc8a6e038cdbf45f574dd8 *man/callPeaks.PeaksAndValleys.Rd
785d452d564af41716e3f8178ae8d004 *man/callXXorXY.numeric.Rd
f761c6b962f69d93855b10613bed6007 *man/cnr.Rd
b178ec0ee62e8bd96cb7656cea5d7826 *man/deShearC1C2.PairedPSCBS.Rd
ef10b0268836641766c037cad9e93917 *man/extractTupleOfDataFiles.MultiSourceCopyNumberNormalization.Rd
e9dc5ced5e166340b30421ee9fd6f219 *man/findAtomicAberrations.CopyNumberRegions.Rd
6401d388710de2c49ec68f9039031afc *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
9e1815089c5a4f22a0a7ee12ce328c78 *man/normalizeBAFsByRegions.PairedPSCBS.Rd
112d603ff11026f9c4d48333c6f3c4b4 *man/normalizeMirroredBAFsByRegions.matrix.Rd
fc9c2fc14d41f9143daf25040317c809 *man/process.MultiSourceCopyNumberNormalization.Rd
1268e29f45b006f5d45bd6170df41211 *man/testAllelicBalanceByBAFs.Rd
