28572fcfccb14de8fdf9b27e22d99189 *DESCRIPTION
c0da7863a96a5197ecd913622f5d7715 *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
689e6c0c1483dc3b73d27b05aec0e62b *R/AbstractCBS.RESTRUCT.R
095d4a26ad877c2fb7a2d342c3eb1a5d *R/CBS.CALL.R
1695e704070060ca9467bb513fc848eb *R/CBS.EXTS.R
d33104664f4fc8057717fd4a21ee0130 *R/CBS.IO.R
e2d9e379bc4ede13612941f5e9999cc0 *R/CBS.PLOT.R
70f0de65256ff8beb73b9ad5eb22b74d *R/CBS.PRUNE.R
516ce96c78b53c21ef955ea5f060f0dc *R/CBS.R
ccfab4f29a7dbb59301d4cb1a894fd85 *R/CBS.RESTRUCT.R
b2b119098e25eadf34eac3facbd43df7 *R/CBS.joinSegments.R
9ba6b8273fcf0381a8cd2adb1b23c9f8 *R/CBS.updateMeansTogether.R
b5d1352116d5019312c4d04c66e0a117 *R/CNA.EXTS.R
2162d34db9d25424f6fd107352e50ed7 *R/DNAcopy.EXTS.R
32a29a708f637b92e714d06c516afc10 *R/PSCBS.EXTS.R
acb4afb8cb1ea536fdec29f26aafa3ef *R/PSCBS.IO.R
3a0c5acdc727bbd576ec817828168e52 *R/PSCBS.RESTRUCT.R
dc14feedeff13e77110cac84ecc90a30 *R/PairedPSCBS.BOOT.R
4ca2dedacb9c3221efdb695a2edc98f9 *R/PairedPSCBS.BOOT2.R
5eb72b38ef68073661b6994ba09bdb35 *R/PairedPSCBS.CALL.R
9f191c150a3ffb6785a76eecb5c30bc6 *R/PairedPSCBS.EXTS.R
6416b0ee77668da9c4f2075461224de4 *R/PairedPSCBS.EXTS3.R
e37f35d71ade59a8e6d5b11e06873bec *R/PairedPSCBS.PLOT.R
10460f9150d5fa2538623c1d2d643a2a *R/PairedPSCBS.PLOT2.R
c3591d90f19fc3b7f351e45b111253aa *R/PairedPSCBS.R
40dcc2cdcdceee701feb5d3aa1e76d40 *R/PairedPSCBS.RESTRUCT.R
1756549a73a3ce773ab836f25e8a51bd *R/PairedPSCBS.applyByRegion.R
958728ec1631ee2cff28e1966d0b3414 *R/PairedPSCBS.callAB.R
158455e10c30b77ec9d4848c7c816b25 *R/PairedPSCBS.callLOH.R
adf7223c984e9b08d6403fa3569bcf0b *R/PairedPSCBS.callROH.R
a9b1f6b2f41fc33f3e24d989bf6e07e0 *R/PairedPSCBS.estimateDeltaAB.R
e21455382b640ec51a24b5647e858cb5 *R/PairedPSCBS.estimateDeltaLOH.R
b24171b05f1448d94158f167656e8988 *R/PairedPSCBS.estimateKappa.R
d882be5f139bbef6fe04283bca1f1eb1 *R/PairedPSCBS.updateMeansTogether.R
fe2d296a073b835f7809640af008709e *R/callSegmentationOutliers.R
4d7a3c9ebe2cc59bc8bbdeda9d4c13d0 *R/drawLevels.DNAcopy.R
3493e6e772feca76014df62373c23f82 *R/findLargeGaps.R
7c4f29a34d1016a37a569af6fa3a34a7 *R/gapsToSegments.R
478b1aa926f57509b2ba1e9530862bdf *R/installDNAcopy.R
e965aa91315bc3667ffb7dd359794cde *R/segmentByCBS.R
bb6a587119892212d0139b84db7a02c5 *R/segmentByPairedPSCBS.R
81b9af5bcfd7a4aca4455cac25b8ed5e *R/testROH.R
75169b11411696abdcb85c284156648f *R/weightedQuantile.R
f01c8d0a982603d34a3df2c76f80c0be *R/zzz.R
ce4048dbb7573c0d87a6e6e25b0b486a *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
9a280a8dda9bd3958e5beab9da70b831 *incl/segmentByPairedPSCBS.Rex
74a37c6532dd5d806f66b5b1029db164 *inst/NEWS
14659728b7be1bb8e37e953a87060e6c *inst/data-ex/PairedPSCBS,exData,chr01.Rbin
04c02b0526868d16389c6bef2f8f5817 *inst/doc/Makefile
9570b3efb4e27043b33dd71622f38ebe *inst/doc/PSCBS.bib
6ceaf175f680707237da0e01a3fe3abf *inst/doc/PairedPSCBS.Rnw.HIDE
e6e7395989cc71a83cca88c299fd7c95 *inst/doc/PairedPSCBS.tex.rsp
f3907cf5bef1f44c8c15558e94274a18 *inst/doc/natbib.bst
a746e9caa4b1782a82f8643cc29be68e *man/AbstractCBS.Rd
9bc505cdf8d3c23542b8bfbdbf5daec7 *man/CBS.Rd
ab62de97e1547d0d71a27db5cabdc917 *man/Non-documented_objects.Rd
e6212eda8859d9633f84bd9196a705e3 *man/PSCBS-package.Rd
a4c4767a0887be22afaa15a19e4aa9d7 *man/PSCBS.Rd
465306997dc7ea9273bd3beae788348f *man/PairedPSCBS.Rd
e902357f561a9cf0ba644d0e4b100e82 *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
ca9a0fa3b9abb182a4ede17191b34c4f *man/callAB.PairedPSCBS.Rd
8ed632d39a9ea660ce996785705aab82 *man/callAllelicBalanceByDH.PairedPSCBS.Rd
a543063831279a93b8b9ba605ed0e31d *man/callAmplifications.CBS.Rd
b71448446a62a5ce2dfde1d836602ab8 *man/callGainsAndLosses.CBS.Rd
790ca7b62182baf7346d316875f486f9 *man/callLOH.PairedPSCBS.Rd
08e8b8ce8abf9d209b050fe9d3b1130e *man/callOutliers.CBS.Rd
78fdc2111ebb18c816d8681f46b50098 *man/callROH.PairedPSCBS.Rd
660796b12fd2a07c079d6f18b1db303b *man/callSegmentationOutliers.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
269cd23287ff2ca9eb7b5eb39963e3d8 *man/findLargeGaps.Rd
3430f0d508edfeb99ed3246c054248c3 *man/gapsToSegments.data.frame.Rd
0c3067c4c4de5e8325009537bca8d1a7 *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
5c074422c311c9c7b04a8901ff09d6d5 *man/save.AbstractCBS.Rd
fc91add727ed1f3deceea5524a8f0d34 *man/segmentByCBS.Rd
915ce0423593b38e4735272f45641e55 *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
e462f2bb0bf3e0a3a74921934e412fcf *tests/segmentByPairedPSCBS.R
