3f79840f7acdd141cf086d1d164a3bae *DESCRIPTION
0bb49848137669b93abdcfc852be65e7 *NAMESPACE
4c5504f490f7fc26549f826014942bdc *R/006.fixVarArgs.R
dcb0e44d79e9859ee6006eb8c70b2837 *R/999.NonDocumentedObjects.R
19cf20a4536986a118f6a32f19ca239f *R/999.package.R
6a9146dcbd7f58c6d1eb134e296080b6 *R/AbstractCBS.HCLUST.R
6373feaf42c95a44532c6dd7bb4aa31b *R/AbstractCBS.PLOT.R
43bd9bd5db0c9d00149ac55367f901be *R/AbstractCBS.PRUNE.R
e08c4ba31071aceef943fcdf8e01f451 *R/AbstractCBS.R
4792140d7fc9e2ba1c5beddcdc522033 *R/AbstractCBS.REPORT.R
aae4d702067914bf4e965ea69d3003ed *R/AbstractCBS.RESTRUCT.R
cb108cc207cc9fa7f67bfcf942821719 *R/CBS.CALL.R
fd98c7669740fb12a797ca513a75dc0f *R/CBS.EXTS.R
f61b1b8e16c6d6acf877dfb0f160f57e *R/CBS.IO.R
7e4a448f8619d739f26bd6fe932ae16c *R/CBS.PLOT,many.R
d256dd851094645f1b9012aab8b6318a *R/CBS.PLOT.R
28d8e644a0c2f899da30bad3577aa20d *R/CBS.PRUNE.R
e53e21cf0f38665d7d02895763ae6150 *R/CBS.R
21e9c6b05f55f2931a2a2537833fe436 *R/CBS.RESTRUCT.R
6220388b477d8992fdb1a4c2681693bd *R/CBS.SMOOTH.R
b2b119098e25eadf34eac3facbd43df7 *R/CBS.joinSegments.R
6c28fb753c160132793c26ae474c36c6 *R/CBS.updateMeansTogether.R
ed080a928098a7ee721079af992f640c *R/CNA.EXTS.R
a58ba133279e7f0f1ecd878234a6e5dc *R/DNAcopy.EXTS.R
571a690b3b1b9d09fe45a122ad1eab66 *R/NonPairedPSCBS.R
07f118d9fd7942687f57c76e3c4f78a3 *R/PSCBS.IO.R
b6a685d3e0233696f4e49bfacdd0c595 *R/PSCBS.R
8990f8e0558b6956d68b38c459891377 *R/PSCBS.RESTRUCT.R
554ff0655e2becfe2b52659499864a38 *R/PairedPSCBS.BOOT,DEPRECATED.R
5a50cb4edcc60d5bc0bd4ecf334f1806 *R/PairedPSCBS.BOOT.R
ca9619224692ddbdb696a702acad2671 *R/PairedPSCBS.CALL.R
4b0c312d2f3647e5ea487fc7f3635f05 *R/PairedPSCBS.EXTS.R
32b2f5f0dc98d1499078587125d93677 *R/PairedPSCBS.EXTS3.R
3c3c2b9ddfe08a5068d20cf0d0381f56 *R/PairedPSCBS.PLOT,many.R
f681ac7af25183c31075111c635575d2 *R/PairedPSCBS.PLOT.R
10460f9150d5fa2538623c1d2d643a2a *R/PairedPSCBS.PLOT2.R
fcc580134d46f0a28634b758cdcc4123 *R/PairedPSCBS.PRUNE.R
8db57a458d181f8532f5f9e34f9a6227 *R/PairedPSCBS.R
7618cc7392081a25b0ac193234b50c7a *R/PairedPSCBS.RESTRUCT.R
1756549a73a3ce773ab836f25e8a51bd *R/PairedPSCBS.applyByRegion.R
ec06725d52ccfc201486eef72dd64ab9 *R/PairedPSCBS.callAB.R
d5ef05cb024aafe6317e2a179da9db10 *R/PairedPSCBS.callCopyNeutral.R
900bb8d6b4ceb964e2512b1e98e7ca7a *R/PairedPSCBS.callGNL.R
d634b46f323cdf8452d8572d9167c5e7 *R/PairedPSCBS.callLOH.R
cd05cd26498f17f945f83f525532a6ef *R/PairedPSCBS.callROH.R
0b6606842467cd1f6e4b58ade02a9e21 *R/PairedPSCBS.estimateDeltaAB.R
ce9cf58a6071007c23c79270fb3da891 *R/PairedPSCBS.estimateDeltaLOH.R
cc3c50a13c6334e2d72f57a28ca5ad9f *R/PairedPSCBS.estimateKappa.R
862baacb79daf6de21305cb2db5c1292 *R/PairedPSCBS.updateMeansTogether.R
3ad6484da80e7e20de112c6f8d3f5621 *R/callSegmentationOutliers.R
4d7a3c9ebe2cc59bc8bbdeda9d4c13d0 *R/drawLevels.DNAcopy.R
0119fe08cdec28314ae4abfa7669dffc *R/exampleData.R
42a8f5da34cee23286d39cc1deed4c25 *R/findCopyNumberNeutralState.R
69cb48e04aadf6487538c4f683848390 *R/findLargeGaps.R
d73ad23cc76c84eafba81a48ac9b7324 *R/gapsToSegments.R
d17ff4d8990661f634e3261343f9a46f *R/installDNAcopy.R
a54218be9ea9f280d6437f75440de350 *R/prememoize.R
3adf189972f9af8a5f7fe43c525db187 *R/segmentByCBS.R
fd3958e95987f11391e186171e898822 *R/segmentByNonPairedPSCBS.R
5b406f9b176e794ac596f51cc134292f *R/segmentByPairedPSCBS.R
70ca04697871ea001289c85ff8231097 *R/testROH.R
9907f449d31281d6ac7357413e2e6ecc *R/weightedQuantile.R
f01c8d0a982603d34a3df2c76f80c0be *R/zzz.R
5a71cab768396edd8384147faf6dff0d *inst/NEWS
14659728b7be1bb8e37e953a87060e6c *inst/data-ex/PairedPSCBS,exData,chr01.Rbin
9570b3efb4e27043b33dd71622f38ebe *inst/doc/PSCBS.bib
7a76d36f65e7920f79f36f2729ef31b6 *inst/doc/PairedPSCBS.R
284d6394ff7ff08340e74809903e4b80 *inst/doc/PairedPSCBS.pdf
de9738f05208507939b4990dade7ad59 *inst/doc/PairedPSCBS.tex.rsp
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
9386fcaafc6de46d5a542f4c1912e5b7 *man/AbstractCBS.Rd
585a665e17aac3a663211235fe628301 *man/CBS.Rd
203b54866233aba6a5fba1bf3b106ddb *man/Non-documented_objects.Rd
ecbc9cedbb1c1905233bcdd8928fc822 *man/NonPairedPSCBS.Rd
08e0d05de49032b30555b7a6c08f53ad *man/PSCBS-package.Rd
0993318c153609197ac38256893860fb *man/PSCBS.Rd
991b11af0147234eeb881d94341239a4 *man/PairedPSCBS.Rd
59ae340fe4e3a601d59da4702ec144fb *man/Restructuring_AbstractCBS_objects.Rd
1f0aab8f0fac7a13036fe42b11d647fe *man/append.AbstractCBS.Rd
36fcd829c96affa6a4a59bc7a70bb3e1 *man/append.CBS.Rd
ea6d26b5b40827c772a6ff8737f79f3a *man/append.PSCBS.Rd
50e341566988e22bef21e831f63bf157 *man/as.CBS.DNAcopy.Rd
22ce4b8908c97ccb56a0f134510bffc3 *man/as.DNAcopy.CBS.Rd
6c583e2926f0ad30c2f396a177e10607 *man/as.data.frame.AbstractCBS.Rd
36905da6829deee76b8c28dcbc4a7d7b *man/as.data.frame.CBS.Rd
6264b550624d39705c29b4b60e557e01 *man/bootstrapTCNandDHByRegion.PairedPSCBS.Rd
6095c6f1db04d7817485853349429489 *man/callAB.PairedPSCBS.Rd
864e191aeab6c265f2181e75c0920faa *man/callAllelicBalanceByDH.PairedPSCBS.Rd
cbba91c4b2701f2f4c19534789a4f972 *man/callAmplifications.CBS.Rd
521539eb523296c1cf58d9364167a161 *man/callCopyNeutral.PairedPSCBS.Rd
efcb9ff1785b2758eb5c9a8bc25b41f1 *man/callCopyNeutralByTCNofAB.PairedPSCBS.Rd
c854e68744cfc82c1fcd8b51ca857fad *man/callGNL.PairedPSCBS.Rd
b1f9fd72e3a1f3e0900d6d2837984b26 *man/callGainsAndLosses.CBS.Rd
dc41bb1efa305ed8e10dc681bc45aa23 *man/callLOH.PairedPSCBS.Rd
2dc88b200365c204d975e1809655af6f *man/callOutliers.CBS.Rd
838dc240a03c12ffe3874864dcf3b22e *man/callROH.PairedPSCBS.Rd
211d3b28082ef8acd6f55539440cb159 *man/callSegmentationOutliers.Rd
af589aed4e4fcf9e491c25a16a2c5c4e *man/dropChangePoints.AbstractCBS.Rd
c2717b3db4da9f95dd8822da6bd689d0 *man/dropRegions.AbstractCBS.Rd
c5db0c489d09bdd39c7b985f91b83514 *man/estimateDeltaAB.PairedPSCBS.Rd
271e67da730c818170d45c7815daa4d4 *man/estimateDeltaABBySmallDH.PairedPSCBS.Rd
a7a6086b85e2a88daf979a3e75abe993 *man/estimateDeltaLOH.PairedPSCBS.Rd
3356c62b92db04ad181b6306d60a87ec *man/estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS.Rd
722d9be399b053a6aa85908186c66617 *man/estimateKappa.PairedPSCBS.Rd
9ea77e7346a6208cf4576bd1d030e756 *man/estimateKappaByC1Density.PairedPSCBS.Rd
ac7446bfe7280633854ace0ce7a43e18 *man/estimateStandardDeviation.CBS.Rd
a8a1368fb2e836d808ab339eec5c3bf7 *man/exampleData.Rd
27a186c28da9718ef148b1d7fdefa315 *man/extractMinorMajorCNs.PairedPSCBS.Rd
2745258268eeffe5d6f8437142a0ca7f *man/extractSegmentMeansByLocus.CBS.Rd
8746af340e1fa0079e418270e7dd31f1 *man/extractTCNAndDHs.PairedPSCBS.Rd
5841980a276a9b98c7529f3fd0b90468 *man/findLargeGaps.Rd
bb5aad4884a0a5481f8c1324dc1b3dc3 *man/findNeutralCopyNumberState.Rd
370ef52d0063f118d951959c33fa2249 *man/gapsToSegments.data.frame.Rd
c27859503bff7a18bdccdb9b900a8837 *man/getCallStatistics.CBS.Rd
7c53a276d0480b1ffce4c937b9c5bf54 *man/getChromosomes.AbstractCBS.Rd
8add6b64fab13e7805e73d454c2f0226 *man/getFractionOfGenomeLost.CBS.Rd
387103384bc6078612b21bb8c6811b2c *man/getLocusData.AbstractCBS.Rd
00e7df1d72be25a848f4f8d4a2b0bec0 *man/getSampleName.AbstractCBS.Rd
18157c31f61c2a4188db12e86e0813e1 *man/getSegments.AbstractCBS.Rd
6890d312647a4c2811bce68f6745d284 *man/getSegments.PSCBS.Rd
b131a212748c753bde39006a4bc1e0c5 *man/getSmoothLocusData.CBS.Rd
402a3c7f52873fa514e9150fc5cbbb7a *man/hclustCNs.AbstractCBS.Rd
12d8023e7c2f8ecc5ca76c7b14381a7a *man/installDNAcopy.Rd
60722d676a3f22a745670e0eff3c011c *man/load.AbstractCBS.Rd
f00dd4af9b09812bdef3bc4cc1961f16 *man/mergeNonCalledSegments.CBS.Rd
cf642a455c7ca06f7072e6ce3ebb1d22 *man/mergeThreeSegments.AbstractCBS.Rd
c50de0e05e4f82bf2f7522e2f1187aa3 *man/mergeTwoSegments.AbstractCBS.Rd
0e699612d7ffa6eb330fff3e1658dbd5 *man/mergeTwoSegments.PairedPSCBS.Rd
f731d643a5fb3eaf98615cfdc04ec678 *man/nbrOfChangePoints.AbstractCBS.Rd
f069cd2ef8345b96302ff3d26f1be080 *man/nbrOfChromosomes.AbstractCBS.Rd
c53be0174950d94d52cb45a196e6ae79 *man/nbrOfLoci.AbstractCBS.Rd
e728c823710b368fa3ddab6a72ba0934 *man/nbrOfSegments.AbstractCBS.Rd
fd7eefda35c1f667ce86552cc380d14d *man/plotTracks.AbstractCBS.Rd
90681d2cbedf4fcc174f9ebadf4ff747 *man/plotTracks.CBS.Rd
17a8ae7c3d0936fdd884c1af40b0c674 *man/plotTracks.PairedPSCBS.Rd
ae6ca7420cb0fca1837b96e407f6b0d6 *man/pruneByDP.AbstractCBS.Rd
eb61680286b462effe4afe72080b25cc *man/pruneByHClust.AbstractCBS.Rd
013127e4dfd9584ce18c9b246c713b50 *man/pruneBySdUndo.CBS.Rd
defd7a96a38e455a8b591fbd6c830b16 *man/report.AbstractCBS.Rd
0c6cedbfc94734758be3257e6a9a120b *man/resetSegments.AbstractCBS.Rd
fd77b2620422811ba4a161325c11c92a *man/save.AbstractCBS.Rd
462cef925fc68e4661732d45149e87ce *man/segmentByCBS.Rd
759f26cd48382e584040bfc448fbe701 *man/segmentByNonPairedPSCBS.Rd
1e4c1fdeb6e4ec17148aeddc2362a169 *man/segmentByPairedPSCBS.Rd
4e6052f570a0117c23ec38b143a30930 *man/setSampleName.AbstractCBS.Rd
a26d814b8b146b036bec5f05585c3f94 *man/testROH.numeric.Rd
e9dd20a0adf9def1b9523d189a35e4f6 *man/updateMeans.AbstractCBS.Rd
79aedb4af12fb676dc87911135275281 *man/updateMeansTogether.AbstractCBS.Rd
f086115f97643a3ca6fac5f20ce01813 *man/weightedQuantile.Rd
b116f4887131fbe471ad7dde0dbfdea9 *man/writeSegments.CBS.Rd
bd91a412e78ba7e79b807a502e20ea23 *man/writeSegments.PSCBS.Rd
997ae33daf5a75e5c0601ebd25545536 *tests/segmentByCBS,knownSegments.R
86ccefa98b37dd6b40cd2cd7e0069f5a *tests/segmentByCBS,report.R
e45abce398a32caf1c25d9c6618824b4 *tests/segmentByCBS,shiftTCN.R
4ffb2b900a7b0e4926a8c03b97b83209 *tests/segmentByNonPairedPSCBS,medianDH.R
079d5f128c5d67d07ef54160109c03cb *tests/segmentByPairedPSCBS,knownSegments.R
edb893ebb774e2f51006fc30e5c06f5b *tests/segmentByPairedPSCBS,noNormalBAFs.R
89daa847cd3181e44db389155c4bdc44 *tests/segmentByPairedPSCBS,report.R
3148b0a6f7da68d10a1ad798d3427001 *tests/segmentByPairedPSCBS,seqOfSegmentsByDP.R
ff1b3680367ad127bc28fd9d24a484b2 *tests/segmentByPairedPSCBS.R
