dd2ea3c39057a858f14c34dfcf707272 *DESCRIPTION
fe01f7bb05791b27925ea36d07715be5 *NAMESPACE
33afdb93d2a0401527c287dac38519cb *NEWS.md
5b3e0291bcc049d9ada9005162c5259a *R/000.R
31cb7684ac252cc553f7a71f77c5cc85 *R/999.DEPRECATED.R
5b9ea216c47a57e772308c8d17cfd10e *R/999.NonDocumentedObjects.R
b9a22d7a3d629919b925558646512bf1 *R/999.package.R
cf11a1bae61124096a25d542b34134b4 *R/AbstractCBS.HCLUST.R
5ee907c9784ccb0408ba4f2c1527d630 *R/AbstractCBS.PLOT.R
3e8ca4bce184866dc280cf1a679946a5 *R/AbstractCBS.PRUNE.R
2a54ff299735ca1ccfd4db9e2d2a3645 *R/AbstractCBS.R
386bdc9fe2dd2c80edbbddf59668128e *R/AbstractCBS.REPORT.R
ca9ed4cca2f5ec2edb971cb2dda9881e *R/AbstractCBS.RESTRUCT.R
ca2fd5e553fd063ba7ff28c3cee6a6f8 *R/AbstractCBS.clearCalls.R
202d73070b48664daed6f8788a523139 *R/CBS.CALL.R
4ef3f9ddda8d6d548ceade99741e884b *R/CBS.EXTS.R
2f9386f71ac98af17eedf88adf2a79eb *R/CBS.IO.R
f173001ac7bb63aa0e8ee4d45b3712d4 *R/CBS.PLOT,many.R
bfb7abec63996fc9b7ddf497651278c5 *R/CBS.PLOT.R
396740d236597cda895e9c2fa0aca6d4 *R/CBS.PRUNE.R
b3d17d661046519219a4d7adc9be4df7 *R/CBS.R
6e7e62087dca79ed0f893c3c692b7867 *R/CBS.RESTRUCT.R
747b0061416ab0fdaef690f524440209 *R/CBS.SMOOTH.R
a01b8fca4229ed36fd40704b294dbbba *R/CBS.joinSegments.R
603ebe88b97bff04472cbc098fb2445d *R/CBS.updateMeansTogether.R
581f27b2999d9c5dd6c6aad2fb2e2390 *R/CNA.EXTS.R
c8bd31ddc050974d23c8093d603b9761 *R/DNAcopy.EXTS.R
8850fc36a815db60e2364229e362600a *R/NonPairedPSCBS.R
a6e072df7c6573a460b6bffdc40fbbab *R/PSCBS.IO.R
a30892181ab7e59b808e36d797979aaf *R/PSCBS.R
8aca0f771027c699cd5dca88c1bee729 *R/PSCBS.RESTRUCT.R
48cc8da528c5bf64c2c15a267c349d7d *R/PSCBS.isLocallyPhased.R
621d9e988de2e8443151fd37950cb7f7 *R/PairedPSCBS.BOOT.R
82bb04a434c11642b0b2a18821a8d258 *R/PairedPSCBS.BOOT.sets.R
279729d2a552aa92757ef82d4ca78a85 *R/PairedPSCBS.CALL.R
3aba4f5259a3dae4bd5ed555b8356631 *R/PairedPSCBS.EXTS.R
70b805fc647b0324bbce1cfcf134ae5b *R/PairedPSCBS.EXTS3.R
c4aafa5a9748db76e61a27e8ca622f7e *R/PairedPSCBS.PLOT,many.R
8100bd2314facc0b6c7339f57e1bc662 *R/PairedPSCBS.PLOT.R
878fe63829f7fda9bbd1db4e359a13ff *R/PairedPSCBS.PLOT2.R
b1e89555e008ec37e13a071e372abfac *R/PairedPSCBS.PRUNE.R
a02aaefa8989d0e9a6ce5027248a31c4 *R/PairedPSCBS.R
0858dae84d1f665d721bd3aa42c3adfe *R/PairedPSCBS.RESTRUCT.R
e50260e3bdb6b891b7093ba2c790ebb8 *R/PairedPSCBS.applyByRegion.R
3458731e78497453c4f663b91c8f0cc5 *R/PairedPSCBS.callAB.R
d7e8145514e3d6be7598493b50a73c72 *R/PairedPSCBS.callCopyNeutral.R
c5a156b8c56e00b734c1ba4528c58331 *R/PairedPSCBS.callGNL.R
dfb8e2ce8ef02f7a9cca0c926e2ef696 *R/PairedPSCBS.callLOH.R
2d94006c4d35dd071042b1e7ef39f15e *R/PairedPSCBS.callROH.R
bb43c1a57b99ed95d3b96663f62397d9 *R/PairedPSCBS.estimateDeltaAB.R
792eead5634c1e8db1323414ec8c12d3 *R/PairedPSCBS.estimateDeltaLOH.R
17eba7b8dd57241e5640b984023a8d6d *R/PairedPSCBS.estimateKappa.R
b9b61ab3388af9481fed61da69fd4067 *R/PairedPSCBS.extractSegmentDataByLocus.R
b643de003b3ce45eac64c32a0a72f032 *R/PairedPSCBS.unTumorBoost.R
eac8ca56b63887e4090f896648516125 *R/PairedPSCBS.updateMeans.R
a0a8ad4af2f7539d1fe67420358695c7 *R/PairedPSCBS.updateMeansTogether.R
39bedc9996acf61a02f81faeed715857 *R/callSegmentationOutliers.R
b1120a7f78a4192dcdcbbcac73c5fcff *R/drawLevels.DNAcopy.R
e51684240cb75a4f3be8a5d3a3c0f04c *R/exampleData.R
3ab3fab527c1f0aecfc607e29f5c2694 *R/findLargeGaps.R
a728221d22ba3203ccb741f5b0771cf5 *R/findNeutralCopyNumberState.R
c58968fa0c597127936f174f2b2c8ad2 *R/gapsToSegments.R
2c523572dd0d3b788bcf65d3bc29d5bb *R/installDNAcopy.R
f5464022de0ba7269fe82fae4e966c15 *R/prememoize.R
a94b36c3f60fc3ae98c749caade5a89c *R/randomSeed.R
b28ad62b69d82b1f464e884ea1ca59b1 *R/segmentByCBS.R
5494355e3295264b6d5ad2eb552ee63b *R/segmentByNonPairedPSCBS.R
a6ff50e418046ea3b4152fa4d6e5b368 *R/segmentByPairedPSCBS.R
cd776ac0c74739ded25b3dafe84cf45a *R/testROH.R
03fddd9ccc07f4b10befa786369c2135 *R/utils.R
65b0bc28aab801c2fbdc93a58be2bbe9 *R/weightedQuantile.R
649ae3161e4d6610a24761ba2aa99d53 *R/writeWIG.R
ec94da06896e5ec37619cce4b4023ec5 *R/zzz.R
4408d3f513bf1b1086c9244303cadc0b *README.md
879fb357b0d8db010ee59babcd7b16bf *build/vignette.rds
3b2cccdbd4eefde2c936639da2c69e5f *inst/CITATION
f738905d2cc4758f4d595bc8c8b4ab5a *inst/WORDLIST
14659728b7be1bb8e37e953a87060e6c *inst/data-ex/PairedPSCBS,exData,chr01.Rbin
c0b189f26030e57c5e59eada84bc2b33 *inst/doc/CBS.R
9bf3a8cca03eb1a147865c702a4413ba *inst/doc/CBS.pdf
6ab8b5697dafb6f0180984df4bf3f5b2 *inst/doc/CBS.tex.rsp
5d3893ffb445a72be4bf07bb234aa5e1 *inst/doc/PairedPSCBS.R
085ec4f52f3720bf6dde4ca967a16057 *inst/doc/PairedPSCBS.pdf
e8d89580cd99dc842d45eb2368ea9bed *inst/doc/PairedPSCBS.tex.rsp
56e6435959f6387651a30e915e54baab *inst/misc/_Rcache/PSCBS/segmentByCBS/sbdry/0109d43cd74c8e7e46db1abde235c808.Rcache
17a5a6d6c343e587021f5e4c7c3ec97e *inst/misc/_Rcache/PSCBS/segmentByCBS/sbdry/2aba5b85ae757609b8b4c9fc60be1156.Rcache
1e03443121d58d43b72492a207272077 *inst/templates/rsp/CBS,report.tex.rsp
f605500742f015ae26c455b37fcc18b8 *inst/templates/rsp/NonPairedPSCBS,report.tex.rsp
008dcc209acfd836649040fa600adbda *inst/templates/rsp/PSCBS.bib
379e54a8d405491faa7e690e414f7b57 *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
7615fd0b844f872869b4afb3bbdfd1bb *inst/templates/rsp/includes/reportSetupMacros.tex.rsp
9b2e313a0483afa2ca60cc616434679f *inst/templates/rsp/includes/sessionInfo.tex.rsp
5abfbbffe381cb5d3d3134f14b45543e *inst/templates/rsp/includes/signalDensities.tex.rsp
4cb7c97012df4c618f08acd20cf1ca63 *inst/templates/rsp/includes/summaryOfAnnotationAndGenotypeCalls.tex.rsp
f3907cf5bef1f44c8c15558e94274a18 *inst/templates/rsp/natbib.bst
186c25ce77ef689100aba5fadc91d9bc *man/AbstractCBS.Rd
7ddee19fcc549f8e7b073b4faaa16924 *man/CBS.Rd
3fcb1c125c14a8680c8498c546de6216 *man/Non-documented_objects.Rd
5e16e2fa4ab9a4c4e6941c72b0f721ff *man/NonPairedPSCBS.Rd
ab0330aa3eae8000ef333c9e41582efb *man/PSCBS-package.Rd
8f716390f47e89519c5ef374ec8f3b00 *man/PSCBS.Rd
8e929052157452c04b7e91bdc1323e11 *man/PairedPSCBS.Rd
91b07ae0f6f46ba1a478921ed2c49b87 *man/Restructuring_AbstractCBS_objects.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
daabd4c3a6e27f7c2d86915b5df84928 *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
3dd1f7945c5b9cd705297dd15aa3232a *man/estimateDeltaAB.PairedPSCBS.Rd
271e67da730c818170d45c7815daa4d4 *man/estimateDeltaABBySmallDH.PairedPSCBS.Rd
d57ec89a054ff04d163a2934d344c15e *man/estimateDeltaCN.PairedPSCBS.Rd
389ecf9619ef23173bae0702a329b719 *man/estimateDeltaLOH.PairedPSCBS.Rd
5c9ac7b578e204c80e175344a5635969 *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
75a127bfd12612ecb73ea6c385e791d9 *man/figures/ex-PSCBS-paired.chr01.png
9dbea07287422753ab5db54fa9b547a4 *man/findLargeGaps.Rd
a05249b87c436c75a0998564f901df85 *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
2652f456e0210bd63ba4928e9cbdd75e *man/getLocusData.AbstractCBS.Rd
e38e4c27a96ad64c745f9db7cb07faa4 *man/getSampleName.AbstractCBS.Rd
3706f46053f67fdc3359d780cd198e7a *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
3e24345d7327bf88fea8b824a582e718 *man/mergeNonCalledSegments.CBS.Rd
cf642a455c7ca06f7072e6ce3ebb1d22 *man/mergeThreeSegments.AbstractCBS.Rd
a3d0413e8e1887c8a3e283128433fe14 *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
b221058f3c0508e8558dd7c68e74cc7c *man/plotTracks1.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
9fa51829a67c564956646e18bf5ec31a *man/segmentByCBS.Rd
d41e05e2d6980cd141885357d2b0072d *man/segmentByNonPairedPSCBS.Rd
031b472a199f8f8d72a2a54826b0bfca *man/segmentByPairedPSCBS.Rd
4c4181efced223c39066439f8741c498 *man/setSampleName.AbstractCBS.Rd
6e9676b9f9825c488bdf96d410cc9539 *man/testROH.numeric.Rd
e9dd20a0adf9def1b9523d189a35e4f6 *man/updateMeans.AbstractCBS.Rd
7d1c1a55ae672f0352ca10e4bd5036ae *man/updateMeansTogether.AbstractCBS.Rd
93205b47f42516cf8c2b66c466ceaca7 *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
b7acfb4684e8a2f6549345a514346807 *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
de7f30135d0e81460dc9bc68fbf958af *tests/segmentByPairedPSCBS,futures.R
b5297118f74861f14db49b1a53eb4d73 *tests/segmentByPairedPSCBS,noNormalBAFs.R
16cae3c29ec03be4526b11b9e5c0a899 *tests/segmentByPairedPSCBS,report.R
07fb3136cfb1d2c93f7a0aeb234a76e6 *tests/segmentByPairedPSCBS,seqOfSegmentsByDP.R
9cdf7cfaa91b475a68f11a56a3c46a99 *tests/segmentByPairedPSCBS.R
6ab8b5697dafb6f0180984df4bf3f5b2 *vignettes/CBS.tex.rsp
2913162b7b2b3081c55f3c36cc43f950 *vignettes/PSCBS.bib
e8d89580cd99dc842d45eb2368ea9bed *vignettes/PairedPSCBS.tex.rsp
f3907cf5bef1f44c8c15558e94274a18 *vignettes/natbib.bst
