902a24282da5d7b160bafe0ee7b74f45 *DESCRIPTION
5247ea511da31f89bab52f2272095f63 *NAMESPACE
4c5504f490f7fc26549f826014942bdc *R/006.fixVarArgs.R
dcb0e44d79e9859ee6006eb8c70b2837 *R/999.NonDocumentedObjects.R
77d1871b32b5caecaf40a1cc0b310e2d *R/999.package.R
50ac20700d5fa203b765d4a685c7829b *R/AbstractCBS.HCLUST.R
c0a25986e9c3065178ca3080b2c39cf8 *R/AbstractCBS.PLOT.R
4403259bfc617fcc4bc789ed0bf964bd *R/AbstractCBS.R
a59ad39294fd4c80c05e23ffabbc52fe *R/AbstractCBS.RESTRUCT.R
c3b03df1ae13b1317c1bc0f5b2962b2b *R/CBS.CALL.R
089a2ec03d2629b107f8546cd13fc2dd *R/CBS.EXTS.R
d33104664f4fc8057717fd4a21ee0130 *R/CBS.IO.R
e2d9e379bc4ede13612941f5e9999cc0 *R/CBS.PLOT.R
70f0de65256ff8beb73b9ad5eb22b74d *R/CBS.PRUNE.R
516ce96c78b53c21ef955ea5f060f0dc *R/CBS.R
9b40bb5995938eeb72433208f68d4887 *R/CBS.RESTRUCT.R
b2b119098e25eadf34eac3facbd43df7 *R/CBS.joinSegments.R
9ba6b8273fcf0381a8cd2adb1b23c9f8 *R/CBS.updateMeansTogether.R
b5d1352116d5019312c4d04c66e0a117 *R/CNA.EXTS.R
2162d34db9d25424f6fd107352e50ed7 *R/DNAcopy.EXTS.R
588529070cf25bd90f919a6e1aa6fcd7 *R/PSCBS.EXTS.R
acb4afb8cb1ea536fdec29f26aafa3ef *R/PSCBS.IO.R
b3e31552d0cd80bdd2b9fa657239ad1e *R/PSCBS.RESTRUCT.R
8167b882f831058a5953a3467263af1c *R/PairedPSCBS.BOOT.R
97f41b1512e939ae871b393fd58f58e5 *R/PairedPSCBS.BOOT2.R
19a386886880191fc68db09d912c123c *R/PairedPSCBS.CALL.R
cfe6eeeba8f6d4fe49fbe4a688159319 *R/PairedPSCBS.EXTS.R
0c17ef67967921dd83b675a001abad2f *R/PairedPSCBS.EXTS3.R
ee84e83923fa3f927f96cb804e550e02 *R/PairedPSCBS.PLOT.R
10460f9150d5fa2538623c1d2d643a2a *R/PairedPSCBS.PLOT2.R
c3591d90f19fc3b7f351e45b111253aa *R/PairedPSCBS.R
23ffbfbbe75ef29261e52e83e05e725b *R/PairedPSCBS.REPORT.R
ce999ad841eb4ed7b6327e4a3e35e3ba *R/PairedPSCBS.RESTRUCT.R
1756549a73a3ce773ab836f25e8a51bd *R/PairedPSCBS.applyByRegion.R
69ec000cd27f6ef10de0df69428eed61 *R/PairedPSCBS.callAB.R
c76db3014368fa71821c5dce9a6e9301 *R/PairedPSCBS.callCN.R
474958bc7085c9398e06f61f016c6482 *R/PairedPSCBS.callGNL.R
e0a239209a1fa00ec77edda08d19b860 *R/PairedPSCBS.callLOH.R
adf7223c984e9b08d6403fa3569bcf0b *R/PairedPSCBS.callROH.R
eae0e65309a825a2b41209e5222b0bc5 *R/PairedPSCBS.estimateDeltaAB.R
a5817a864ab4a60879fe9cae2da08939 *R/PairedPSCBS.estimateDeltaLOH.R
b24171b05f1448d94158f167656e8988 *R/PairedPSCBS.estimateKappa.R
d882be5f139bbef6fe04283bca1f1eb1 *R/PairedPSCBS.updateMeansTogether.R
abd4f603438f1221ce84ac9a06d76fa8 *R/callSegmentationOutliers.R
4d7a3c9ebe2cc59bc8bbdeda9d4c13d0 *R/drawLevels.DNAcopy.R
9b9e5a4d061cb4e4b46d397194b200df *R/findCopyNumberNeutralState.R
c14707fe317c431c7d8e04b94c01e8a8 *R/findLargeGaps.R
65c442356ddb3e24e6725be2ae4720b8 *R/gapsToSegments.R
478b1aa926f57509b2ba1e9530862bdf *R/installDNAcopy.R
c7415c9cfe5dbbde26067a5a2ffe2808 *R/segmentByCBS.R
a420311d24263abc0aa65387b7f79716 *R/segmentByPairedPSCBS.R
81b9af5bcfd7a4aca4455cac25b8ed5e *R/testROH.R
75169b11411696abdcb85c284156648f *R/weightedQuantile.R
f01c8d0a982603d34a3df2c76f80c0be *R/zzz.R
400834adb90ede445249b0b5159656a7 *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
dc159f9c2616b75b4b5d3bf11c3a4fb4 *incl/segmentByCBS,knownSegments.Rex
72cfc381225ddf435e75ed25665228ed *incl/segmentByCBS,plot.Rex
ef802d1b1dd25c013a023146b8d26582 *incl/segmentByCBS,pruneBySdUndo.Rex
2fee3bd8377a866383d2c084587edb78 *incl/segmentByCBS,tests.Rex
d41b7fc96024349135ff3a8b8f0495d5 *incl/segmentByCBS.Rex
d6686b397e75aa8b3ad185a4bdd47211 *incl/segmentByPairedPSCBS,allLOH.Rex
03f068c699fb7e62bc998750a92d5944 *incl/segmentByPairedPSCBS,report.Rex
9a280a8dda9bd3958e5beab9da70b831 *incl/segmentByPairedPSCBS.Rex
6bb02f0e17f2ed7e1b78cebf9a969146 *inst/NEWS
14659728b7be1bb8e37e953a87060e6c *inst/data-ex/PairedPSCBS,exData,chr01.Rbin
9570b3efb4e27043b33dd71622f38ebe *inst/doc/PSCBS.bib
6ceaf175f680707237da0e01a3fe3abf *inst/doc/PairedPSCBS.Rnw
c1af4aead581bb53d1168526c4d5ce46 *inst/doc/PairedPSCBS.pdf
9dade9d0ebbcfbb24c99531cb49ff506 *inst/doc/PairedPSCBS.tex.rsp
1ccfaccf73356cbdcfad931d98b0d318 *inst/doc/index.html
5dc6a2219efcb71d4a68d5ebba905527 *inst/templates/rsp/PSCBS.bib
331db95e416240af18c51a9367208e06 *inst/templates/rsp/PairedPSCBSReport.tex.rsp
f01bbc88ade170e0dcb4c76fac17fe7d *inst/templates/rsp/bioinformatics-journals-abbr.bib
f3907cf5bef1f44c8c15558e94274a18 *inst/templates/rsp/natbib.bst
a746e9caa4b1782a82f8643cc29be68e *man/AbstractCBS.Rd
61165c31e4836987c9c089774b7b4331 *man/CBS.Rd
2af496a531e1e228c7b1fe8d41d111a9 *man/Non-documented_objects.Rd
fd978f7c36bd0b414cf29dc239c569e4 *man/PSCBS-package.Rd
7b22db8c0f7245db400f1027f4df338b *man/PSCBS.Rd
68c07b6cc3e4da1e894b3c10aa6baef0 *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
0d01b93e5e2d06d06d9364d5d32e4f2f *man/callCN.PairedPSCBS.Rd
999a6dd5b36a8fb804e964df2cb1627a *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
5d912f14d362fe680758cc5265cae4da *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
53b08ff78ec4552ca2966eb55ad41ca6 *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
86fbb6964990962a70fd4a7dbb26752b *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
2309acda2e46fe8bb8861e2627d8827f *man/pruneByHClust.AbstractCBS.Rd
c2f5cfb9494ddf35ded84fcbdfcaa1f2 *man/pruneBySdUndo.CBS.Rd
7ce7ff1bec5af276b4bf572420298597 *man/report.PairedPSCBS.Rd
5c074422c311c9c7b04a8901ff09d6d5 *man/save.AbstractCBS.Rd
61052ec2e89e7df29a3638d025615407 *man/segmentByCBS.Rd
71f49f727d8638a629b6a3e4295591da *man/segmentByPairedPSCBS.Rd
9bea8c4866bcea0e06f4b997af52048b *man/setSampleName.AbstractCBS.Rd
b78eedfdb7e34f0f6339afaa9643a4e1 *man/updateMeansTogether.AbstractCBS.Rd
8e080ad61ad5afa8cc0f2ca8890bded5 *man/weightedQuantile.Rd
9a0c5167abfdc16b9b73fd8b63bddb6a *man/writeSegments.CBS.Rd
0b402039ea39811dd68f0f7fa5a3bba2 *man/writeSegments.PSCBS.Rd
025000ca99e4ca6502a3fec3a1d48b25 *tests/segmentByCBS,knownSegments.R
7db4a379c61b0eba6a239faf503f0f5a *tests/segmentByPairedPSCBS,knownSegments.R
3077feb8b844a1097b7e729dc4028cae *tests/segmentByPairedPSCBS,noNormalBAFs.R
024df597f2cd3f6eefb3a54dec9e5e7a *tests/segmentByPairedPSCBS,report.R
b14d895f1fa090974a1c6daf9a657616 *tests/segmentByPairedPSCBS.R
