17371be9817b3321b070dab898bc45c7 *DESCRIPTION
04ac1709a30151853db03d9c269e7552 *NAMESPACE
732b3581cd9ba8780eb6a8d598c459ec *NEWS
5b3e0291bcc049d9ada9005162c5259a *R/000.R
367ea8aa78bc210b9f197e26644fee25 *R/006.fixVarArgs.R
31cb7684ac252cc553f7a71f77c5cc85 *R/999.DEPRECATED.R
5b9ea216c47a57e772308c8d17cfd10e *R/999.NonDocumentedObjects.R
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5ee907c9784ccb0408ba4f2c1527d630 *R/AbstractCBS.PLOT.R
4fedce8daaf114c72c3341875d5c6ee2 *R/AbstractCBS.PRUNE.R
185cbd87c6f903d7c50369222c6f6e33 *R/AbstractCBS.R
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2f9386f71ac98af17eedf88adf2a79eb *R/CBS.IO.R
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747b0061416ab0fdaef690f524440209 *R/CBS.SMOOTH.R
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8c15a6b78f1e40bb5b09946cbd9dfabf *R/DNAcopy.EXTS.R
1b2e9ca5ae843323f10b9b1a64d0fdb7 *R/NonPairedPSCBS.R
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58813bab92c47ce2a0acc01dc436efa3 *R/PairedPSCBS.EXTS.R
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0c59448b6f9e6fe59c35f1d1b985a7f8 *R/PairedPSCBS.R
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3345c2f4970de508146f10a9ef78daf9 *R/PairedPSCBS.applyByRegion.R
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4ac6cdacfd153c003b4a6059ef534bbe *R/PairedPSCBS.callCopyNeutral.R
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0a5bdcaa615385cce91a2878c36b8ef2 *R/PairedPSCBS.estimateDeltaAB.R
baaafb33e91764cdefae48373f817175 *R/PairedPSCBS.estimateDeltaLOH.R
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8be987fadcfc82e027128c30f0131f38 *R/PairedPSCBS.extractSegmentDataByLocus.R
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63dd3e5f10552013ec2d60a989b686e1 *R/PairedPSCBS.updateMeans.R
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39bedc9996acf61a02f81faeed715857 *R/callSegmentationOutliers.R
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e51684240cb75a4f3be8a5d3a3c0f04c *R/exampleData.R
e9da5817a70792d2f38860ac4ec05880 *R/findLargeGaps.R
c9dea9a3f5f925d33e13182c0eee623c *R/findNeutralCopyNumberState.R
ccafc5d2d243b5c84dbbd68a8612c19c *R/gapsToSegments.R
e4433cf34635a54911e3278ac14ea823 *R/installDNAcopy.R
f5464022de0ba7269fe82fae4e966c15 *R/prememoize.R
a94b36c3f60fc3ae98c749caade5a89c *R/randomSeed.R
20210b25cb7afad0be544b0342a5d244 *R/segmentByCBS.R
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56a63b22ba27644ac792736ad9831693 *R/segmentByPairedPSCBS.R
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5ee2b122fff0b4bbb486d96a2589d9cd *R/weightedQuantile.R
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ec94da06896e5ec37619cce4b4023ec5 *R/zzz.R
33a315073bbcc9ad7ea904d09e7b0886 *build/vignette.rds
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5a64ec853e1015d3f57d3c6985bcc7fe *inst/doc/CBS.R
b90bb1de3a8f18a07785da088920a235 *inst/doc/CBS.pdf
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2d2c639e0d72962658f270675cccbf0b *inst/templates/rsp/includes/pscnSegmentationTracks.tex.rsp
c72a4a967345e999cccdaeb0b072d01d *inst/templates/rsp/includes/pscnSegmentationTransitions.tex.rsp
860859b29771b6fade80e4d0cebc59d6 *inst/templates/rsp/includes/references.tex.rsp
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9a88214a9db5b94992ea733bb8c6157f *inst/templates/rsp/includes/signalDensities.tex.rsp
4cb7c97012df4c618f08acd20cf1ca63 *inst/templates/rsp/includes/summaryOfAnnotationAndGenotypeCalls.tex.rsp
f3907cf5bef1f44c8c15558e94274a18 *inst/templates/rsp/natbib.bst
2b56d0468b9f942e57503501a0bd04eb *man/AbstractCBS.Rd
c57d135382604d98c61c9886b980f7c4 *man/CBS.Rd
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ab0330aa3eae8000ef333c9e41582efb *man/PSCBS-package.Rd
0b394f22e118ad065d7cfa087466f84a *man/PSCBS.Rd
53147935dd77ee4b9bfdecc395a5b4e2 *man/PairedPSCBS.Rd
59ae340fe4e3a601d59da4702ec144fb *man/Restructuring_AbstractCBS_objects.Rd
34c29070d119a8ac679e7772fa2e2458 *man/append.AbstractCBS.Rd
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22ce4b8908c97ccb56a0f134510bffc3 *man/as.DNAcopy.CBS.Rd
a6cb223758bc39c5d9ca4e7157c410dd *man/as.data.frame.AbstractCBS.Rd
53f2d1c6fc28166ff5cb62e476fea136 *man/as.data.frame.CBS.Rd
bd714c1f380fd2889fea937384d961fc *man/bootstrapTCNandDHByRegion.PairedPSCBS.Rd
5881cd9aafe6ff57de60b17ecd69cc00 *man/c.CBS.Rd
6095c6f1db04d7817485853349429489 *man/callAB.PairedPSCBS.Rd
69c7ae7eccf16bfebf15bada46d6721c *man/callAllelicBalanceByDH.PairedPSCBS.Rd
8a177a1d31c63dcd3e3cf1aaab45b07b *man/callAmplifications.CBS.Rd
521539eb523296c1cf58d9364167a161 *man/callCopyNeutral.PairedPSCBS.Rd
419ed670fb8422053a9e44a41b1eef6f *man/callCopyNeutralByTCNofAB.PairedPSCBS.Rd
c854e68744cfc82c1fcd8b51ca857fad *man/callGNL.PairedPSCBS.Rd
9fc634c7d99b5ad734bc1057bfcca1bb *man/callGainsAndLosses.CBS.Rd
dc41bb1efa305ed8e10dc681bc45aa23 *man/callLOH.PairedPSCBS.Rd
732b27351d445addf7bbf2b99e654b36 *man/callOutliers.CBS.Rd
838dc240a03c12ffe3874864dcf3b22e *man/callROH.PairedPSCBS.Rd
b347080d29b70bc29aff1ff8934a28b3 *man/callSegmentationOutliers.Rd
af589aed4e4fcf9e491c25a16a2c5c4e *man/dropChangePoints.AbstractCBS.Rd
c2717b3db4da9f95dd8822da6bd689d0 *man/dropRegions.AbstractCBS.Rd
927c0252a746ca7baa3f6e70c94984ac *man/estimateDeltaAB.PairedPSCBS.Rd
271e67da730c818170d45c7815daa4d4 *man/estimateDeltaABBySmallDH.PairedPSCBS.Rd
d57ec89a054ff04d163a2934d344c15e *man/estimateDeltaCN.PairedPSCBS.Rd
a7a6086b85e2a88daf979a3e75abe993 *man/estimateDeltaLOH.PairedPSCBS.Rd
bd5b73e4f84a670dce9a9ee060b3bafa *man/estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS.Rd
722d9be399b053a6aa85908186c66617 *man/estimateKappa.PairedPSCBS.Rd
e25d09950c2ac2aed8932081db2dc0eb *man/estimateKappaByC1Density.PairedPSCBS.Rd
bbca3a25a2700e1040065c966c28036c *man/estimateStandardDeviation.CBS.Rd
a8a1368fb2e836d808ab339eec5c3bf7 *man/exampleData.Rd
dd702d33c6c9dc7c8a61db7d8e57d7e8 *man/extractMinorMajorCNs.PairedPSCBS.Rd
2745258268eeffe5d6f8437142a0ca7f *man/extractSegmentMeansByLocus.CBS.Rd
da4cb348dce202b19542a681c3b0a893 *man/extractTCNAndDHs.PairedPSCBS.Rd
9dbea07287422753ab5db54fa9b547a4 *man/findLargeGaps.Rd
aa2f91382cb975e1886c2d0a439aba90 *man/findNeutralCopyNumberState.Rd
3699de1bee98ca4afbbfa4b93e27175a *man/gapsToSegments.data.frame.Rd
1bd0c24ae698ca98b9e691a6b9099a73 *man/getBootstrapLocusSets.PairedPSCBS.Rd
c27859503bff7a18bdccdb9b900a8837 *man/getCallStatistics.CBS.Rd
01be02b70f50acdf32af74d1095bdee8 *man/getChromosomes.AbstractCBS.Rd
8add6b64fab13e7805e73d454c2f0226 *man/getFractionOfGenomeLost.CBS.Rd
0c00f0a1b5c95157e300a92455e38669 *man/getLocusData.AbstractCBS.Rd
e38e4c27a96ad64c745f9db7cb07faa4 *man/getSampleName.AbstractCBS.Rd
6f07ef6692ece0549fcabe4e63bc8832 *man/getSegments.AbstractCBS.Rd
6d48429ce911acae62ce59a708e623ca *man/getSegments.PSCBS.Rd
2d45f3dfbe49462191da53f7d04341ab *man/getSmoothLocusData.CBS.Rd
2aa35c71d6043956970e091489a23ce4 *man/hclustCNs.AbstractCBS.Rd
12d8023e7c2f8ecc5ca76c7b14381a7a *man/installDNAcopy.Rd
c668b9975804d67f833e671635dab54b *man/joinSegments.CBS.Rd
280fcc003932b9bc7aea70ef5a61f74f *man/load.AbstractCBS.Rd
3e24345d7327bf88fea8b824a582e718 *man/mergeNonCalledSegments.CBS.Rd
cf642a455c7ca06f7072e6ce3ebb1d22 *man/mergeThreeSegments.AbstractCBS.Rd
c50de0e05e4f82bf2f7522e2f1187aa3 *man/mergeTwoSegments.AbstractCBS.Rd
8ea75fe5a459f8b6502e75b6f6ee6eb0 *man/mergeTwoSegments.PairedPSCBS.Rd
8e33b404462d57fa8111ec6c17def975 *man/nbrOfChangePoints.AbstractCBS.Rd
e1913743bcf8545b5c7f3cf9b206624d *man/nbrOfChromosomes.AbstractCBS.Rd
b05c91b6528f5dfb200d1493523b3525 *man/nbrOfLoci.AbstractCBS.Rd
32dc5a786239d886939b19a814ea865c *man/nbrOfSegments.AbstractCBS.Rd
420bef7918487909706f01ac02d1f7b0 *man/normalizeTotalCNs.AbstractCBS.Rd
b1618d544720f032c95f6563a53fc645 *man/ploidy.AbstractCBS.Rd
285605d73ea6b1ad80d561642b2d5644 *man/plotTracks.AbstractCBS.Rd
8e407ed8348a1ad6e1276c7c8d9a3c41 *man/plotTracks.CBS.Rd
17a8ae7c3d0936fdd884c1af40b0c674 *man/plotTracks.PairedPSCBS.Rd
00e5e824765da4e97788ad6f5764e2ec *man/pruneByDP.AbstractCBS.Rd
525e01e468a4599c41af3a300f25362a *man/pruneByHClust.AbstractCBS.Rd
013127e4dfd9584ce18c9b246c713b50 *man/pruneBySdUndo.CBS.Rd
0cc1a3f744dae1ca53c07f4fb61e91e6 *man/randomSeed.Rd
6ac688a354724df8e0b3c5110949ca21 *man/report.AbstractCBS.Rd
88b05c630f8af9a2437df4a846bab343 *man/resetSegments.AbstractCBS.Rd
c5008992920a8e9f86507297712cdfb1 *man/save.AbstractCBS.Rd
9fa51829a67c564956646e18bf5ec31a *man/segmentByCBS.Rd
b3fb1177bdb0fc8680745b9315392ad9 *man/segmentByNonPairedPSCBS.Rd
b0343a718160b28dda064d64c1e3ff59 *man/segmentByPairedPSCBS.Rd
4c4181efced223c39066439f8741c498 *man/setSampleName.AbstractCBS.Rd
6e9676b9f9825c488bdf96d410cc9539 *man/testROH.numeric.Rd
e9dd20a0adf9def1b9523d189a35e4f6 *man/updateMeans.AbstractCBS.Rd
79aedb4af12fb676dc87911135275281 *man/updateMeansTogether.AbstractCBS.Rd
a39ac96df7c724ddfa623f152881e647 *man/weightedQuantile.Rd
63a7356f7ad4433a9361ecee5ae683c2 *man/writeSegments.CBS.Rd
c17aa26ce4bed7b08417b45882e96276 *man/writeSegments.PSCBS.Rd
de8847124d8ea6cdaddb1f52269f10b0 *tests/PairedPSCBS,boot.R
a20d5e74b660794a207ebee3b146e571 *tests/findLargeGaps.R
4f1a9d8d791a7a899eb18e19b56a98ca *tests/randomSeed.R
41267a6a75014b780037272409dcf4a4 *tests/segmentByCBS,calls.R
b2da6ee74152a817eff407a3f9801d82 *tests/segmentByCBS,futures.R
f04ed0148cf6f6b62c2af44ccdbdb7e4 *tests/segmentByCBS,median.R
2237835c4c7d3019d0fb50a86efc5604 *tests/segmentByCBS,prune.R
db249f1f339e184e651a68ea57033834 *tests/segmentByCBS,report.R
de09c8c008c4bde1691e8c7e4e30fb82 *tests/segmentByCBS,shiftTCN.R
4770dcbd22a8f1f0aa7ec339059eda83 *tests/segmentByCBS,weights.R
8437c7366d535981f316bd770123ea74 *tests/segmentByCBS.R
065319c9e5582cb4b5c7ea4b9bbbc793 *tests/segmentByNonPairedPSCBS,medianDH.R
d8cd7bdf20f657bcc393c55c7bce382e *tests/segmentByPairedPSCBS,DH.R
d03756cf4f3124b51ddc4b1a7ee224ff *tests/segmentByPairedPSCBS,calls.R
15142ca045a6ffd63736e52feadc73cf *tests/segmentByPairedPSCBS,futures.R
b5297118f74861f14db49b1a53eb4d73 *tests/segmentByPairedPSCBS,noNormalBAFs.R
16cae3c29ec03be4526b11b9e5c0a899 *tests/segmentByPairedPSCBS,report.R
07fb3136cfb1d2c93f7a0aeb234a76e6 *tests/segmentByPairedPSCBS,seqOfSegmentsByDP.R
9cdf7cfaa91b475a68f11a56a3c46a99 *tests/segmentByPairedPSCBS.R
406cb30de5806a646ef620a16a0b9a40 *vignettes/CBS.tex.rsp
0930d1c2145468247525d7faf3fdd9d3 *vignettes/PSCBS.bib
883540936ac195cb8c5fe864f8059a17 *vignettes/PairedPSCBS.tex.rsp
f3907cf5bef1f44c8c15558e94274a18 *vignettes/natbib.bst
