449db7c5bb30a58b192d505077c15ade *DESCRIPTION
2f05a3c24eb00e9468998fca19e553cc *NAMESPACE
6ae47c9a2acc33d3bd42573894b424a8 *NEWS
5b3e0291bcc049d9ada9005162c5259a *R/000.R
3e3dabecfb506b75e8e24743c5336630 *R/006.fixVarArgs.R
93c57de5b16270cd0c7bbbe4de701afc *R/999.DEPRECATED.R
dcb0e44d79e9859ee6006eb8c70b2837 *R/999.NonDocumentedObjects.R
b9a22d7a3d629919b925558646512bf1 *R/999.package.R
69783c0bd5d2e16d00019fcbc2b6cd42 *R/AbstractCBS.HCLUST.R
42b2df2eaa3f0ee53e9107a25f0611df *R/AbstractCBS.PLOT.R
de26d3c861c7d471ebd70a7d7d2fa6c9 *R/AbstractCBS.PRUNE.R
7f61f82f030a54635051670cbaaca601 *R/AbstractCBS.R
08250793df9a159d63a1e7adb635fd78 *R/AbstractCBS.REPORT.R
1b2c6f96ec322260ac94db8a24ade7eb *R/AbstractCBS.RESTRUCT.R
172afe9107992b6a440aff2423dff4f7 *R/AbstractCBS.clearCalls.R
60d8a792c8ee78ee78f9d9efc8d02c06 *R/CBS.CALL.R
edfd54b4775d77a44226c981d7d17c97 *R/CBS.EXTS.R
3c0853753de1a1c3f330d6d587a08c19 *R/CBS.IO.R
c310e53e773254cd9ac6c59bb2c1783a *R/CBS.PLOT,many.R
1ed40336d8cee4e68e94e7735ae765b4 *R/CBS.PLOT.R
d8c5c4d518d2567815342e50a2462403 *R/CBS.PRUNE.R
1ec8dedcb31b0d7931d34e29c89e5945 *R/CBS.R
07098fd3c3d3d1bf1ae5acd465ed622b *R/CBS.RESTRUCT.R
6cbb38b5afda180074d6e7ae6944f1c2 *R/CBS.SMOOTH.R
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ed080a928098a7ee721079af992f640c *R/CNA.EXTS.R
04b1f858cbf28fe53a3694d74631bb39 *R/DNAcopy.EXTS.R
92b7a3bae2008d66f12352f4404d62e7 *R/NonPairedPSCBS.R
07f118d9fd7942687f57c76e3c4f78a3 *R/PSCBS.IO.R
2d2f785ee6453b24cffe8db0ec9dff6f *R/PSCBS.R
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51ac012b54a436f4192527683b7d4c83 *R/PairedPSCBS.BOOT.R
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12d7aba84aa278fcb9a4ab47ccf82a9a *R/PairedPSCBS.CALL.R
dd623ca14fe0a21a348eca8c20867cf1 *R/PairedPSCBS.EXTS.R
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9d975e71e9269ca60ed7cf9c157b9071 *R/PairedPSCBS.PLOT,many.R
04f0c08b47c62a47bd93e117465ff50f *R/PairedPSCBS.PLOT.R
35856c69684d43d40064ecca1cbd76b1 *R/PairedPSCBS.PLOT2.R
fcc580134d46f0a28634b758cdcc4123 *R/PairedPSCBS.PRUNE.R
ee8250dd910ee73c76018091c3cacfcb *R/PairedPSCBS.R
e6aac8ff4746b3ae3f3ac23bc39bfb0c *R/PairedPSCBS.RESTRUCT.R
2f5897a3b46d4c7f8a55ca424ef91113 *R/PairedPSCBS.applyByRegion.R
695e0ebc76969b3b2fdbbe659fbb118c *R/PairedPSCBS.callAB.R
cec62197be140cc333383631f96580b6 *R/PairedPSCBS.callCopyNeutral.R
3cbbee95b70484bbb76215158fb518e4 *R/PairedPSCBS.callGNL.R
c85b32a324461b8e96ef01ae33b0b6c1 *R/PairedPSCBS.callLOH.R
83077bc1d08afdc3a8f62a240f0a96f1 *R/PairedPSCBS.callROH.R
0b6606842467cd1f6e4b58ade02a9e21 *R/PairedPSCBS.estimateDeltaAB.R
dc6744d8ae34728ab082853ef9fdaac2 *R/PairedPSCBS.estimateDeltaLOH.R
bc3d5fe7f8ee8eacc93904ba71ade982 *R/PairedPSCBS.estimateKappa.R
bd7fdb3fbb5b5e7d875fa7a4b4169b26 *R/PairedPSCBS.extractSegmentDataByLocus.R
16ff2709a944fcf57934b9f98d6ab39b *R/PairedPSCBS.unTumorBoost.R
6e9246055b7995fc0f5a893e96d04c3f *R/PairedPSCBS.updateMeans.R
feaa3831a43ec7136765e09cff90f6d9 *R/PairedPSCBS.updateMeansTogether.R
2e67b46e69bfc82000a563d198d9c07d *R/callSegmentationOutliers.R
4d7a3c9ebe2cc59bc8bbdeda9d4c13d0 *R/drawLevels.DNAcopy.R
0119fe08cdec28314ae4abfa7669dffc *R/exampleData.R
e1ae515bff38833400454f077c8260e7 *R/findLargeGaps.R
4e8025349a3933694913a4f784162692 *R/findNeutralCopyNumberState.R
6668141241a50eb225890ca7cce13a7d *R/gapsToSegments.R
d48f6ff09d630cac23b3db8d5819e216 *R/installDNAcopy.R
71483b466dfb355f14ad5d4ce9ed0233 *R/prememoize.R
9bd61b757a7ce40f2dc5288c91e62a63 *R/randomSeed.R
3e3abeec541a7f336bec2a44be41d01e *R/segmentByCBS.R
da90c04cddc9f3d4c7253ddadf83d9fc *R/segmentByNonPairedPSCBS.R
4fc7cc8c0b4d3e35fddb24bc2466da58 *R/segmentByPairedPSCBS.R
7d1907ae7ab66a48b4eded1d496b277b *R/testROH.R
acea5de06a39f1fa395f67b8cb4700a3 *R/weightedQuantile.R
10f35ac9acf7767891662bf19f626506 *R/writeWIG.R
be48c341685be130b84a86685bdd2888 *R/zzz.R
02b6cddb26cfa7274d32611663cd4697 *build/vignette.rds
022d11168732e10dffbdc9ced980a7ab *inst/CITATION
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c74d4ed48e817db1390d66db934f6b1d *inst/doc/CBS.R
6edcd28a28b97243b2c45d7c1e253c6b *inst/doc/CBS.pdf
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824561cd7837b185bc5f557834a69e56 *inst/doc/PairedPSCBS.R
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f605500742f015ae26c455b37fcc18b8 *inst/templates/rsp/NonPairedPSCBS,report.tex.rsp
008dcc209acfd836649040fa600adbda *inst/templates/rsp/PSCBS.bib
c1defeedca4dc2d1885a712b349d539d *inst/templates/rsp/PairedPSCBS,report.tex.rsp
f01bbc88ade170e0dcb4c76fac17fe7d *inst/templates/rsp/bioinformatics-journals-abbr.bib
5146f637b61e03ac550811e9d46de420 *inst/templates/rsp/includes/levelDensities.tex.rsp
2d2c639e0d72962658f270675cccbf0b *inst/templates/rsp/includes/pscnSegmentationTracks.tex.rsp
c72a4a967345e999cccdaeb0b072d01d *inst/templates/rsp/includes/pscnSegmentationTransitions.tex.rsp
860859b29771b6fade80e4d0cebc59d6 *inst/templates/rsp/includes/references.tex.rsp
7885a06ef57438e704c0d9d35dddc716 *inst/templates/rsp/includes/reportHeader.tex.rsp
9a68af6ca781e60d82670869008ffe33 *inst/templates/rsp/includes/reportSetupGraphics.tex.rsp
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9b2e313a0483afa2ca60cc616434679f *inst/templates/rsp/includes/sessionInfo.tex.rsp
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
a859f536fc78af70a787fd8c9cf0f589 *man/CBS.Rd
701811475cc198b3b5a689835a62eda9 *man/Non-documented_objects.Rd
0fabcd673135f35b19bde7c2e7a60957 *man/NonPairedPSCBS.Rd
ab0330aa3eae8000ef333c9e41582efb *man/PSCBS-package.Rd
7d0dec180dd8506f471862d40a20eb4b *man/PSCBS.Rd
4cae1b60885af021c08a91e1756641c4 *man/PairedPSCBS.Rd
59ae340fe4e3a601d59da4702ec144fb *man/Restructuring_AbstractCBS_objects.Rd
1f0aab8f0fac7a13036fe42b11d647fe *man/append.AbstractCBS.Rd
0e47e730083c1af44f4378fa3329807d *man/append.CBS.Rd
e79d626f47c80e89160221840e45b01c *man/append.PSCBS.Rd
e534107eb35ccbb5e59093d2acf6e32c *man/as.CBS.DNAcopy.Rd
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
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
2dc88b200365c204d975e1809655af6f *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
6f6b2594eeddd7a2d7f131e738ea0778 *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
ae6ca7420cb0fca1837b96e407f6b0d6 *man/pruneByDP.AbstractCBS.Rd
517f08eb913a6e8c058b0f60780fe1d2 *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
ee4f795b8db9d32656d8e71c67f6e7f7 *man/segmentByCBS.Rd
b3fb1177bdb0fc8680745b9315392ad9 *man/segmentByNonPairedPSCBS.Rd
92577da258a8b83cb775754eb87db6d7 *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
ab15d5fe78bd1fad10ef763923e6ec79 *tests/segmentByCBS,futures.R
f04ed0148cf6f6b62c2af44ccdbdb7e4 *tests/segmentByCBS,median.R
2237835c4c7d3019d0fb50a86efc5604 *tests/segmentByCBS,prune.R
31fc411fec814fe4d12ff9b59772c9d0 *tests/segmentByCBS,report.R
d497c25b629338a58a4816d3a9755fe5 *tests/segmentByCBS,shiftTCN.R
4770dcbd22a8f1f0aa7ec339059eda83 *tests/segmentByCBS,weights.R
b6b41f53af25eb3d23d9423b3b18386c *tests/segmentByCBS.R
065319c9e5582cb4b5c7ea4b9bbbc793 *tests/segmentByNonPairedPSCBS,medianDH.R
d8cd7bdf20f657bcc393c55c7bce382e *tests/segmentByPairedPSCBS,DH.R
d03756cf4f3124b51ddc4b1a7ee224ff *tests/segmentByPairedPSCBS,calls.R
41e564dfd0c35bc9c6f65df676d44948 *tests/segmentByPairedPSCBS,futures.R
b5297118f74861f14db49b1a53eb4d73 *tests/segmentByPairedPSCBS,noNormalBAFs.R
f548d6f682c19df3fb6e5872dff37686 *tests/segmentByPairedPSCBS,report.R
5e2e0e0355667f0e403ae854ed6292b2 *tests/segmentByPairedPSCBS,seqOfSegmentsByDP.R
f0aeff863889c75b9ffbdcf1fe675724 *tests/segmentByPairedPSCBS.R
406cb30de5806a646ef620a16a0b9a40 *vignettes/CBS.tex.rsp
0930d1c2145468247525d7faf3fdd9d3 *vignettes/PSCBS.bib
883540936ac195cb8c5fe864f8059a17 *vignettes/PairedPSCBS.tex.rsp
f3907cf5bef1f44c8c15558e94274a18 *vignettes/natbib.bst
