b6953ced9ca72a17fed8e1e3c1703a1a *DESCRIPTION
5247ea511da31f89bab52f2272095f63 *NAMESPACE
4c5504f490f7fc26549f826014942bdc *R/006.fixVarArgs.R
dcb0e44d79e9859ee6006eb8c70b2837 *R/999.NonDocumentedObjects.R
77d1871b32b5caecaf40a1cc0b310e2d *R/999.package.R
62568247d6f2616dfcd73e1b75abb0ba *R/AbstractCBS.HCLUST.R
c0a25986e9c3065178ca3080b2c39cf8 *R/AbstractCBS.PLOT.R
fe39e56ff4098e4fc0c000c9621aa243 *R/AbstractCBS.PRUNE.R
a568968db45d3f09caa0d8a2bc8ad9f8 *R/AbstractCBS.R
13da1bb43e59345aef65799d54bf7f4b *R/AbstractCBS.REPORT.R
e9a3326d4afe46decbbf1ae4d0262de5 *R/AbstractCBS.RESTRUCT.R
c3b03df1ae13b1317c1bc0f5b2962b2b *R/CBS.CALL.R
93d4e460faaf57af09bd3e663ed0bdf9 *R/CBS.EXTS.R
d33104664f4fc8057717fd4a21ee0130 *R/CBS.IO.R
d5315b8fdf85bcad0569845da9d4a3cb *R/CBS.PLOT.R
7204edd59ba4fe58f6a5568996ec8063 *R/CBS.PRUNE.R
dc5435ffda1b884d40f04a9f1b75758c *R/CBS.R
bc186616695d22a55db714a107b7f973 *R/CBS.RESTRUCT.R
b2b119098e25eadf34eac3facbd43df7 *R/CBS.joinSegments.R
9ba6b8273fcf0381a8cd2adb1b23c9f8 *R/CBS.updateMeansTogether.R
ed080a928098a7ee721079af992f640c *R/CNA.EXTS.R
4ae500bb6fcdf8e9a601e8eddf120637 *R/DNAcopy.EXTS.R
f7699590cdfb9279e0cfe4aa85f668e5 *R/NonPairedPSCBS.R
acb4afb8cb1ea536fdec29f26aafa3ef *R/PSCBS.IO.R
6ac9927fd22419572f26ebfc7aaa6076 *R/PSCBS.R
207618fe50f8922d1389130f420494d2 *R/PSCBS.RESTRUCT.R
1336433bbb0d56e65ccd37f53e6f6419 *R/PairedPSCBS.BOOT.R
1f5795bd52d7c7545b1c31b8cb498729 *R/PairedPSCBS.BOOT2.R
be28bccc13da1ae53b417a27168ce228 *R/PairedPSCBS.CALL.R
d6a7893ccb470d1a528a1ad00b5c5f0f *R/PairedPSCBS.EXTS.R
32b2f5f0dc98d1499078587125d93677 *R/PairedPSCBS.EXTS3.R
1c63c7869bfd8d6a3ff300a4634fea97 *R/PairedPSCBS.PLOT.R
10460f9150d5fa2538623c1d2d643a2a *R/PairedPSCBS.PLOT2.R
fcc580134d46f0a28634b758cdcc4123 *R/PairedPSCBS.PRUNE.R
18b7a9fe8e0598c3936b6aa879a8a49e *R/PairedPSCBS.R
ce999ad841eb4ed7b6327e4a3e35e3ba *R/PairedPSCBS.RESTRUCT.R
1756549a73a3ce773ab836f25e8a51bd *R/PairedPSCBS.applyByRegion.R
3b3c0c65359171a8783a23a714c3faa1 *R/PairedPSCBS.callAB.R
0743b9bbd24f97a455c17d0ea2b9fc02 *R/PairedPSCBS.callCopyNeutral.R
474958bc7085c9398e06f61f016c6482 *R/PairedPSCBS.callGNL.R
9e17559357c3606844b0038c1ff10554 *R/PairedPSCBS.callLOH.R
c80b018bee3710703467725f4ad767c7 *R/PairedPSCBS.callROH.R
eae0e65309a825a2b41209e5222b0bc5 *R/PairedPSCBS.estimateDeltaAB.R
53d07478c49863f7db012ec769bbd7ba *R/PairedPSCBS.estimateDeltaLOH.R
eee18de8d5399edd9c47a302d594850a *R/PairedPSCBS.estimateKappa.R
d882be5f139bbef6fe04283bca1f1eb1 *R/PairedPSCBS.updateMeansTogether.R
abd4f603438f1221ce84ac9a06d76fa8 *R/callSegmentationOutliers.R
4d7a3c9ebe2cc59bc8bbdeda9d4c13d0 *R/drawLevels.DNAcopy.R
64aeee41c71b8983b2da027a715c70eb *R/findCopyNumberNeutralState.R
c14707fe317c431c7d8e04b94c01e8a8 *R/findLargeGaps.R
4bd4656bd52eddbcab5f5a93c8bb43f0 *R/gapsToSegments.R
478b1aa926f57509b2ba1e9530862bdf *R/installDNAcopy.R
a54218be9ea9f280d6437f75440de350 *R/prememoize.R
77db6e2260bf30539c3621493d3b3441 *R/segmentByCBS.R
046b533ea320872346f36528de81d2a6 *R/segmentByNonPairedPSCBS.R
59e2c7330a3d59732368b6e4befe9a09 *R/segmentByPairedPSCBS.R
385ac4ae273c0d858654b11f52b0e242 *R/testROH.R
b662b58f131ae9418a5267e4f7522b94 *R/weightedQuantile.R
f01c8d0a982603d34a3df2c76f80c0be *R/zzz.R
f4acca405d0f368209d0adf34540c853 *incl/999.missingdocs.txt
28122107c97ed62b29c7ccb213d9deee *incl/BengtssonH_etal_2010.Rd
2bcd843fc81f4d736b7e430c0e75ce9b *incl/OlshenA_etal_2011.Rd
5a707f9030b99348ebedf539761ad2f6 *incl/OlshenVenkatraman_2004.Rd
2cb15227fc9da636150e12c696f285ac *incl/VenkatramanOlshen_2007.Rd
332e31533688e5a4ffb6c33549ab6db3 *incl/as.DNAcopy.Rex
ddd6775f71e632d908435128efc7762b *incl/segmentByCBS,calls.Rex
8ec9ae6507547ac904d1c40e92a825d2 *incl/segmentByCBS,knownSegments.Rex
72cfc381225ddf435e75ed25665228ed *incl/segmentByCBS,plot.Rex
ef802d1b1dd25c013a023146b8d26582 *incl/segmentByCBS,pruneBySdUndo.Rex
0b1384de13c174b9cda33c7a8d84d5b4 *incl/segmentByCBS,tests.Rex
d41b7fc96024349135ff3a8b8f0495d5 *incl/segmentByCBS.Rex
4072a161c7670eb8a9c114e2f1046854 *incl/segmentByNonPairedPSCBS.Rex
573fd3c79c51e30920571232165caf10 *incl/segmentByPairedPSCBS,HetsAndHoms.Rex
663387ee215dd6962e68e29899a0041f *incl/segmentByPairedPSCBS,allLOH.Rex
18fb653dfa34effdb4bbcc6cacdcfc7c *incl/segmentByPairedPSCBS.Rex
07eb71157aae31f2ec3b8ae66b61016c *inst/NEWS
14659728b7be1bb8e37e953a87060e6c *inst/data-ex/PairedPSCBS,exData,chr01.Rbin
f1887e2275ba4f6fe5d24cb91e77b535 *inst/doc/CBS.tex.rsp
9570b3efb4e27043b33dd71622f38ebe *inst/doc/PSCBS.bib
6ceaf175f680707237da0e01a3fe3abf *inst/doc/PairedPSCBS.Rnw
569f9938ee3a9650e457efac4fc9c372 *inst/doc/PairedPSCBS.pdf
057b4215f43f522348795ce09a6287ae *inst/doc/PairedPSCBS.tex.rsp
1ccfaccf73356cbdcfad931d98b0d318 *inst/doc/index.html
56e6435959f6387651a30e915e54baab *inst/misc/_Rcache/PSCBS/segmentByCBS/sbdry/0109d43cd74c8e7e46db1abde235c808.Rcache
17a5a6d6c343e587021f5e4c7c3ec97e *inst/misc/_Rcache/PSCBS/segmentByCBS/sbdry/2aba5b85ae757609b8b4c9fc60be1156.Rcache
a0e77366d90649bf447893a5d2fd52d9 *inst/templates/rsp/CBS,report.tex.rsp
313b9ff0929f2b10ec647bea95be8295 *inst/templates/rsp/PSCBS.bib
f32e008a5e2542f1fdc38f0a79d43dc5 *inst/templates/rsp/PairedPSCBS,report.tex.rsp
f01bbc88ade170e0dcb4c76fac17fe7d *inst/templates/rsp/bioinformatics-journals-abbr.bib
f3907cf5bef1f44c8c15558e94274a18 *inst/templates/rsp/natbib.bst
acc6991116573afd14bf3f18467d7a4d *man/AbstractCBS.Rd
4ad09ca8e1dce43c2a39b3659a780a13 *man/CBS.Rd
a226b5f991f7c9944d7ec4e820dc9b12 *man/Non-documented_objects.Rd
c7b70e36a44c0ea25384b3ac3baf8921 *man/NonPairedPSCBS.Rd
c3c7e2c3cf236ac8a2ed96016f6c0626 *man/PSCBS-package.Rd
b6f68f262d5f006893b9f65c3281a37a *man/PSCBS.Rd
516f5d8b3733871e7f1ddc7024b835e2 *man/PairedPSCBS.Rd
8cbbf2739309b1f377a4a1a3739d42a2 *man/Restructuring_AbstractCBS_objects.Rd
58c7a2524f3eac570d0fea8cceb842bd *man/append.AbstractCBS.Rd
53224e9276d05b1f34b38e170f5147b5 *man/append.CBS.Rd
e57f86f50fe0f07254fdf02e22967d4f *man/append.PSCBS.Rd
118a61b10b45e019100947f467cedb36 *man/as.CBS.DNAcopy.Rd
c75206c4f9cc9976562bc4118ac8b72e *man/as.DNAcopy.CBS.Rd
06367aa0a12ce644ee7dce80824e3708 *man/as.data.frame.AbstractCBS.Rd
fccb7ad0c6000c747c4d0a55c4164acf *man/as.data.frame.CBS.Rd
87ad0c8c7327869b0bb69fc600575a72 *man/callAB.PairedPSCBS.Rd
8ed632d39a9ea660ce996785705aab82 *man/callAllelicBalanceByDH.PairedPSCBS.Rd
a543063831279a93b8b9ba605ed0e31d *man/callAmplifications.CBS.Rd
447245ff87f139e294354f7801b6a417 *man/callCopyNeutral.PairedPSCBS.Rd
6830f0370811703e510b245bb3c75d65 *man/callCopyNeutralByTCNofAB.PairedPSCBS.Rd
0a6a3a1ceba95e8bf764a851559a3592 *man/callGNL.PairedPSCBS.Rd
2e3cfdef7653c587750cde90073b5199 *man/callGainsAndLosses.CBS.Rd
d12a76c715b3c044bf73dd38df9d85f9 *man/callLOH.PairedPSCBS.Rd
08e8b8ce8abf9d209b050fe9d3b1130e *man/callOutliers.CBS.Rd
78fdc2111ebb18c816d8681f46b50098 *man/callROH.PairedPSCBS.Rd
660796b12fd2a07c079d6f18b1db303b *man/callSegmentationOutliers.Rd
69d49a15369e3eaf6446391726435460 *man/dropChangePoints.AbstractCBS.Rd
d76c62648e2118cd50334e633fa5d923 *man/dropRegions.AbstractCBS.Rd
87db0f192c2c31921d588733b80b15bd *man/estimateDeltaAB.PairedPSCBS.Rd
1617ccd97dc5e6beb6fb64b0fe2bfd70 *man/estimateDeltaABBySmallDH.PairedPSCBS.Rd
ed65c56ad6e423f2bd65b3bbb5c96fda *man/estimateDeltaLOH.PairedPSCBS.Rd
9e9c068c1d3d41e195c13f578a8cd919 *man/estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS.Rd
360585bbf44e605f4f9fe9095cc1d1a9 *man/estimateKappa.PairedPSCBS.Rd
5f2eb364b95c4fadc9e642780e7f1bb2 *man/estimateKappaByC1Density.PairedPSCBS.Rd
ba6b67c6f52662d173097ddb439d5ca0 *man/estimateStandardDeviation.CBS.Rd
3a84554e65f5cb459e114e163937a2ae *man/extractMinorMajorCNs.PairedPSCBS.Rd
28de52eff83e97b604ca8d61afd65fb9 *man/extractSegmentMeansByLocus.CBS.Rd
5072e82910bfe25d9e000f9e45ab257b *man/extractTCNAndDHs.PairedPSCBS.Rd
68c31a388fde8297a265dc42b381860b *man/findLargeGaps.Rd
d9c706305cd154385bc22d3a9976aefc *man/findNeutralCopyNumberState.Rd
5887e399489e3165c25fe5892e3be41d *man/gapsToSegments.data.frame.Rd
1dc41ceb0c4721bb39872949479ca64d *man/getCallStatistics.CBS.Rd
bcf57cf704fd6f4892787d78341b4f4f *man/getChromosomes.AbstractCBS.Rd
ff250f5a0c943c9d2558df7d074c2eba *man/getFractionOfGenomeLost.CBS.Rd
80597f99643517ab1de4b347de216945 *man/getLocusData.AbstractCBS.Rd
0ca0a123fff6772544f5f871cbfbd17f *man/getSampleName.AbstractCBS.Rd
acf6828c67bf5bd5b79367215ac2f812 *man/getSegments.AbstractCBS.Rd
2fef0f76a23a3728196fa0281c1b21a3 *man/getSegments.PSCBS.Rd
f54e6480290e72170cbe8fd2ce5c3dac *man/hclustCNs.AbstractCBS.Rd
3148099f30753ebcd091b818cd4375cc *man/installDNAcopy.Rd
f4159cf0116d248bbf317d017396bd5d *man/load.AbstractCBS.Rd
d5c26d36f656d4bff5f4b6c80ae778a5 *man/mergeNonCalledSegments.CBS.Rd
e6321e429da7e45356bf688d55cdf78c *man/mergeThreeSegments.AbstractCBS.Rd
a43138768865aaa1afe4bc94fe40e996 *man/mergeTwoSegments.AbstractCBS.Rd
1bfea9398686e6af211ca0f32155d951 *man/mergeTwoSegments.PairedPSCBS.Rd
59715aafb4c8c79d1183c095e0dc21ae *man/nbrOfChangePoints.AbstractCBS.Rd
7bede6c0987148a477410cfdda4c56b9 *man/nbrOfChromosomes.AbstractCBS.Rd
9e2646d6bba6c522cd57d28bc3b680d0 *man/nbrOfLoci.AbstractCBS.Rd
d17e225d817de471fdb28ed28ff3346a *man/nbrOfSegments.AbstractCBS.Rd
60c1fe4c7a997aafb500bc283658767c *man/plotTracks.AbstractCBS.Rd
326cb5838a2f145a625b055de3eb8d54 *man/plotTracks.CBS.Rd
a67164f008a128ac19af8caf51139a1d *man/plotTracks.PairedPSCBS.Rd
83d5847669394df437013b3bc6d49598 *man/pruneByDP.AbstractCBS.Rd
09a2ef8508ef8c29391470901f72f0a4 *man/pruneByHClust.AbstractCBS.Rd
c2f5cfb9494ddf35ded84fcbdfcaa1f2 *man/pruneBySdUndo.CBS.Rd
6bbb8cf039c77d770610e1281a5766b6 *man/report.AbstractCBS.Rd
5c074422c311c9c7b04a8901ff09d6d5 *man/save.AbstractCBS.Rd
05fb2b5de82b4246d2acc96c51ce60f8 *man/segmentByCBS.Rd
5b96c327c884b9ed0803e215ee98c5d7 *man/segmentByNonPairedPSCBS.Rd
206034938c2b62e6a26f9815c4076cf9 *man/segmentByPairedPSCBS.Rd
9bea8c4866bcea0e06f4b997af52048b *man/setSampleName.AbstractCBS.Rd
e632b8674b369600af715193df031bbd *man/updateMeans.AbstractCBS.Rd
2e194a404d5c830cec53a23bdf3f736c *man/updateMeansTogether.AbstractCBS.Rd
a4595216c6f444f8e9bfd6b1c562e6f5 *man/weightedQuantile.Rd
9a0c5167abfdc16b9b73fd8b63bddb6a *man/writeSegments.CBS.Rd
0b402039ea39811dd68f0f7fa5a3bba2 *man/writeSegments.PSCBS.Rd
997ae33daf5a75e5c0601ebd25545536 *tests/segmentByCBS,knownSegments.R
19954a05fc9e20f1a2ecb52a675fcb30 *tests/segmentByCBS,report.R
e5658c535458bff3616074f1edde6306 *tests/segmentByCBS,shiftTCN.R
e5299b949e1c6bac48501c20bf35166d *tests/segmentByPairedPSCBS,knownSegments.R
3077feb8b844a1097b7e729dc4028cae *tests/segmentByPairedPSCBS,noNormalBAFs.R
024df597f2cd3f6eefb3a54dec9e5e7a *tests/segmentByPairedPSCBS,report.R
523962b8185977851bc342790fb3aa7e *tests/segmentByPairedPSCBS,seqOfSegmentsByDP.R
b14d895f1fa090974a1c6daf9a657616 *tests/segmentByPairedPSCBS.R
