b512bb2c9bc7f4cdebd26d6968798790 *DESCRIPTION
8d2ef73f693647c13ef7cd9dc640ea0e *NAMESPACE
4c5504f490f7fc26549f826014942bdc *R/006.fixVarArgs.R
dcb0e44d79e9859ee6006eb8c70b2837 *R/999.NonDocumentedObjects.R
59f45d3fc49e6a7a82821dc57708339e *R/999.package.R
e96efbb88ad117cd1d18e22e79af3970 *R/AbstractCBS.HCLUST.R
42b2df2eaa3f0ee53e9107a25f0611df *R/AbstractCBS.PLOT.R
39af7d0143e80f94a6a1f1f64acbd2a8 *R/AbstractCBS.PRUNE.R
140a30e2071fae15815e0e948910fa8c *R/AbstractCBS.R
f735ae1c4b716aa6b907f6abb5adf640 *R/AbstractCBS.REPORT.R
5d8eb2dbd66d540096d3d72b90876d2e *R/AbstractCBS.RESTRUCT.R
037fe7af33876e0dfd4f47ed3fd66544 *R/CBS.CALL.R
f339cdf70339de3e3e1ead0757412314 *R/CBS.EXTS.R
f61b1b8e16c6d6acf877dfb0f160f57e *R/CBS.IO.R
ea9863281396e50023055aa3f85775bb *R/CBS.PLOT,many.R
34870a18d493ed8e959a1bcd508cb78b *R/CBS.PLOT.R
23b1f082269847d8368f85bed80be92b *R/CBS.PRUNE.R
7a824197146425ee37fef102cfad04a3 *R/CBS.R
b803150d41927c1aa5bcea6cf9d4daf9 *R/CBS.RESTRUCT.R
f6b30fd4d4ea2b94e000200acd9ed7eb *R/CBS.SMOOTH.R
b2b119098e25eadf34eac3facbd43df7 *R/CBS.joinSegments.R
6c28fb753c160132793c26ae474c36c6 *R/CBS.updateMeansTogether.R
ed080a928098a7ee721079af992f640c *R/CNA.EXTS.R
a58ba133279e7f0f1ecd878234a6e5dc *R/DNAcopy.EXTS.R
25776e562d762de0f8b5eb950f4fb615 *R/NonPairedPSCBS.R
07f118d9fd7942687f57c76e3c4f78a3 *R/PSCBS.IO.R
b6a685d3e0233696f4e49bfacdd0c595 *R/PSCBS.R
a2fcd9252c9e1aae1c982a81e9c9eaad *R/PSCBS.RESTRUCT.R
483b46500305d31a6a1f4e3ae42ef4ae *R/PairedPSCBS.BOOT,DEPRECATED.R
079831316b9dda170f8cfb20e878065f *R/PairedPSCBS.BOOT.R
dc3ed47c532e07bb9d6a1735eea17649 *R/PairedPSCBS.CALL.R
fb97b691932164bbd459879c9833baf6 *R/PairedPSCBS.EXTS.R
32b2f5f0dc98d1499078587125d93677 *R/PairedPSCBS.EXTS3.R
7ff4700c726e189c66dc86bd874690b7 *R/PairedPSCBS.PLOT,many.R
3b9a44c9af271f772f597eaa3d7a5db2 *R/PairedPSCBS.PLOT.R
47dcfe1d48ec4c9b546b0d9ebf57b6bb *R/PairedPSCBS.PLOT2.R
fcc580134d46f0a28634b758cdcc4123 *R/PairedPSCBS.PRUNE.R
a4a9a5459a52c53af408da69c8c86779 *R/PairedPSCBS.R
86e8a3c062615e692418e369dd252b38 *R/PairedPSCBS.RESTRUCT.R
1756549a73a3ce773ab836f25e8a51bd *R/PairedPSCBS.applyByRegion.R
695e0ebc76969b3b2fdbbe659fbb118c *R/PairedPSCBS.callAB.R
b97a4026a701a02761648251cc084eb2 *R/PairedPSCBS.callCopyNeutral.R
3cc1b36f1313187a0a146900183ab877 *R/PairedPSCBS.callGNL.R
c85b32a324461b8e96ef01ae33b0b6c1 *R/PairedPSCBS.callLOH.R
9111c0d3ae7a6752706b3bd443deee3c *R/PairedPSCBS.callROH.R
0b6606842467cd1f6e4b58ade02a9e21 *R/PairedPSCBS.estimateDeltaAB.R
48a8053f7e1962928960fd3df32870f7 *R/PairedPSCBS.estimateDeltaLOH.R
cca4c22a4f61ced4b50703ef40cbf9a5 *R/PairedPSCBS.estimateKappa.R
862baacb79daf6de21305cb2db5c1292 *R/PairedPSCBS.updateMeansTogether.R
3ad6484da80e7e20de112c6f8d3f5621 *R/callSegmentationOutliers.R
4d7a3c9ebe2cc59bc8bbdeda9d4c13d0 *R/drawLevels.DNAcopy.R
0119fe08cdec28314ae4abfa7669dffc *R/exampleData.R
0d0c4d1f5e1e783aa6af626a1dcbe30d *R/findLargeGaps.R
4e7daaaace0e71589cf300643a4ca3dc *R/findNeutralCopyNumberState.R
808709d6818e1fd7f6a9018e72bfff75 *R/gapsToSegments.R
d48f6ff09d630cac23b3db8d5819e216 *R/installDNAcopy.R
a54218be9ea9f280d6437f75440de350 *R/prememoize.R
1e3c5a9ac1f4bd5b08686fd4cfcb3524 *R/segmentByCBS.R
2ae4a79796deb09b23d265e662b06944 *R/segmentByNonPairedPSCBS.R
44e87d88a77f03bc4e4bcf9fc8aa73bc *R/segmentByPairedPSCBS.R
70ca04697871ea001289c85ff8231097 *R/testROH.R
4daad48c133c984e376c58e18506b7a3 *R/weightedQuantile.R
70f5174a45a80fb0b48618aacf216bd9 *R/zzz.R
40ba12d2d796c5edf3bf491d9b7d5943 *build/vignette.rds
4a412c41d2a18bda2346362dc7411220 *inst/NEWS
14659728b7be1bb8e37e953a87060e6c *inst/data-ex/PairedPSCBS,exData,chr01.Rbin
b7c48ec7fedd1d59512d534b8a1431c1 *inst/doc/CBS.R
97d425d5739ee50a4ce2e49f08e0f3af *inst/doc/CBS.pdf
ac2816bea69f738d29eaab5a5c4cfd08 *inst/doc/CBS.tex.rsp
9570b3efb4e27043b33dd71622f38ebe *inst/doc/PSCBS.bib
ff501c485bdbd682410e5cb16a6440fb *inst/doc/PairedPSCBS.R
263e3e247a11b3a8471772191fb8bf65 *inst/doc/PairedPSCBS.pdf
4f83696d6d776ab55e58cc729fbd3b29 *inst/doc/PairedPSCBS.tex.rsp
f3907cf5bef1f44c8c15558e94274a18 *inst/doc/natbib.bst
56e6435959f6387651a30e915e54baab *inst/misc/_Rcache/PSCBS/segmentByCBS/sbdry/0109d43cd74c8e7e46db1abde235c808.Rcache
17a5a6d6c343e587021f5e4c7c3ec97e *inst/misc/_Rcache/PSCBS/segmentByCBS/sbdry/2aba5b85ae757609b8b4c9fc60be1156.Rcache
ccd6bcf757884d5a0a9623ec2191aa27 *inst/templates/rsp/CBS,report.tex.rsp
f605500742f015ae26c455b37fcc18b8 *inst/templates/rsp/NonPairedPSCBS,report.tex.rsp
313b9ff0929f2b10ec647bea95be8295 *inst/templates/rsp/PSCBS.bib
32ab5a9037c3890ba4207897708d9971 *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
8e547dde182d7daac5fd88b8e665fe52 *inst/templates/rsp/includes/reportSetupGraphics.tex.rsp
7615fd0b844f872869b4afb3bbdfd1bb *inst/templates/rsp/includes/reportSetupMacros.tex.rsp
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
9a4176daa8f3309780052a492b521949 *man/AbstractCBS.Rd
7634aab5499fc892b8954e809eafe4b2 *man/CBS.Rd
203b54866233aba6a5fba1bf3b106ddb *man/Non-documented_objects.Rd
f3a12216fdf7a8f382b396c674f358ce *man/NonPairedPSCBS.Rd
dc9e4369df2a73e635e85907de377eca *man/PSCBS-package.Rd
9c9afb6359bd943a890a1005928a5101 *man/PSCBS.Rd
bbbe04a7aaf2d1b9aad0b3e91da89b05 *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
76326cc7c44d10b4f76573144e7c34a6 *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
5828bca8d9a54c162cb383af7a97fd4e *man/callSegmentationOutliers.Rd
af589aed4e4fcf9e491c25a16a2c5c4e *man/dropChangePoints.AbstractCBS.Rd
c2717b3db4da9f95dd8822da6bd689d0 *man/dropRegions.AbstractCBS.Rd
927c0252a746ca7baa3f6e70c94984ac *man/estimateDeltaAB.PairedPSCBS.Rd
271e67da730c818170d45c7815daa4d4 *man/estimateDeltaABBySmallDH.PairedPSCBS.Rd
a7a6086b85e2a88daf979a3e75abe993 *man/estimateDeltaLOH.PairedPSCBS.Rd
bd5b73e4f84a670dce9a9ee060b3bafa *man/estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS.Rd
722d9be399b053a6aa85908186c66617 *man/estimateKappa.PairedPSCBS.Rd
2297bca99b9819e398054ee6a1dd6c0e *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
cd7e5c0bf40f059455aac72d67fc3a89 *man/findLargeGaps.Rd
aa2f91382cb975e1886c2d0a439aba90 *man/findNeutralCopyNumberState.Rd
c0335cc834973eb92513bbd021e39d65 *man/gapsToSegments.data.frame.Rd
c27859503bff7a18bdccdb9b900a8837 *man/getCallStatistics.CBS.Rd
01be02b70f50acdf32af74d1095bdee8 *man/getChromosomes.AbstractCBS.Rd
8add6b64fab13e7805e73d454c2f0226 *man/getFractionOfGenomeLost.CBS.Rd
30563f7e411518417bad1c2eca14b27b *man/getLocusData.AbstractCBS.Rd
e38e4c27a96ad64c745f9db7cb07faa4 *man/getSampleName.AbstractCBS.Rd
895613b449c67004ee013acfb8da3498 *man/getSegments.AbstractCBS.Rd
6890d312647a4c2811bce68f6745d284 *man/getSegments.PSCBS.Rd
b131a212748c753bde39006a4bc1e0c5 *man/getSmoothLocusData.CBS.Rd
5ab3cd2adb212d820b2bf5f24450ce20 *man/hclustCNs.AbstractCBS.Rd
12d8023e7c2f8ecc5ca76c7b14381a7a *man/installDNAcopy.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
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
1a8209880aa9e4f09ea175b4048bc504 *man/pruneByHClust.AbstractCBS.Rd
013127e4dfd9584ce18c9b246c713b50 *man/pruneBySdUndo.CBS.Rd
13e387543a8e5fa5fb53197e6c44ee16 *man/report.AbstractCBS.Rd
88b05c630f8af9a2437df4a846bab343 *man/resetSegments.AbstractCBS.Rd
c5008992920a8e9f86507297712cdfb1 *man/save.AbstractCBS.Rd
acf665dac40547c8cc33864d3d635d89 *man/segmentByCBS.Rd
51b0a822944ed5e8471b148a1246320c *man/segmentByNonPairedPSCBS.Rd
f6a59623637c54cd7578db0949ac5524 *man/segmentByPairedPSCBS.Rd
4c4181efced223c39066439f8741c498 *man/setSampleName.AbstractCBS.Rd
a26d814b8b146b036bec5f05585c3f94 *man/testROH.numeric.Rd
e9dd20a0adf9def1b9523d189a35e4f6 *man/updateMeans.AbstractCBS.Rd
79aedb4af12fb676dc87911135275281 *man/updateMeansTogether.AbstractCBS.Rd
a39ac96df7c724ddfa623f152881e647 *man/weightedQuantile.Rd
38adac958d91151b46f84f728547a248 *man/writeSegments.CBS.Rd
c17aa26ce4bed7b08417b45882e96276 *man/writeSegments.PSCBS.Rd
d3245dae8f4a3d3f7a88434766ba175a *tests/segmentByCBS,knownSegments.R
86ccefa98b37dd6b40cd2cd7e0069f5a *tests/segmentByCBS,report.R
6b3afbf3601687067cc8955a97db6fd4 *tests/segmentByCBS,shiftTCN.R
81a2be60cc21cd9eb49c6fff555542a9 *tests/segmentByNonPairedPSCBS,medianDH.R
079d5f128c5d67d07ef54160109c03cb *tests/segmentByPairedPSCBS,knownSegments.R
edb893ebb774e2f51006fc30e5c06f5b *tests/segmentByPairedPSCBS,noNormalBAFs.R
89daa847cd3181e44db389155c4bdc44 *tests/segmentByPairedPSCBS,report.R
3c6f435b86c4b39ee388aafabe70a553 *tests/segmentByPairedPSCBS,seqOfSegmentsByDP.R
ff1b3680367ad127bc28fd9d24a484b2 *tests/segmentByPairedPSCBS.R
