36c260178b473f985d1331273484d982 *DESCRIPTION
8022aa26e14b2f0a6b6b29e16ca9ac94 *NAMESPACE
65938cc8b21b2fa28a9c474b26280ada *R/DMRcaller.R
d3db4e254050962c19aa6bf803ac0152 *R/ONTdata.R
1cc64f082ef388f6014b8c3a5292cff9 *R/Replicates.R
86acf08758184589592ee5f39029a6cb *R/computeCoMethylatedPostions.R
725dcc85042031ba2959bf8269b3f83e *R/computeCoMethylatedRegions.R
ce4e91e502dc79386836f571e17eb5c0 *R/computeDMRs.R
e94638053e59e84d3b4331941c715c52 *R/computePMDs.R
a090e44c507cccfa08a929360ba4a306 *R/computeVMDs.R
9334181b093e64451c91422ade4ac5e4 *R/coverage.R
42f19969b0b50984423944a25ac48bda *R/extractGC.R
28fda1662823643c4211ab5bb4764a1d *R/filterVMRsONT.R
d1b7b4a83a924ca82e3aed8ee91e2815 *R/generalFunctions.R
2ea92e159f961dcdc4e88cc57a058dfa *R/loadData.R
54f6d808e7ccd23adf571ddc707c5ccc *R/localProfile.R
63ee8dc16ed343085cb8c6eca9275b00 *R/movingAverage.R
0c8c43705a1fe5334fb5747ffa5a6646 *R/profile.R
a7f13d1d1fa31c6bc407af00f60550d4 *R/regions.R
5f197e534492cd2e7a2c4e6a0ed27331 *R/spatialCorrelation.R
bcf1e555f19a4a0c77f77f3e082338ba *R/statisticalTests.R
744a899517e5c74cf3f4241478c4ce6e *build/vignette.rds
1c8211047fa13376845e7f3956155713 *data/DMRsNoiseFilterCG.RData
8f0fad11ada832a94df73e5769a01aa2 *data/GEs.RData
4c27b4446f35aaa364288cc7af787f1e *data/GEs_hg38.RData
f992e3fd671817f45653e10c0d4c770d *data/PMDsBinsCG.RData
43c8112cee381de1b33cc398e7270749 *data/PMDsNoiseFilterCG.RData
d88b1272159019fa3efa975c819891fc *data/datalist
df3d2b4a2be049d24bb51f05d1cc079e *data/methylationDataList.RData
620e384af0cb0f2b4b95b8e07948f5d9 *data/ontSampleGRangesList.RData
1090b1f47148d53ce38db449be12418c *data/ont_gr_GM18870_chr1_PMD_bins_1k.RData
6596c072138e658feb36e7b9e9c00a5f *data/ont_gr_GM18870_chr1_sorted_bins_1k.RData
b2db81d597dc8db4312d8d54fa388a55 *data/syntheticDataReplicates.RData
5b81fb4d1878a998a73845e942fc22e0 *inst/CITATION
4e4b5d676c2ab13a25c46ef07909fb17 *inst/NEWS
980b3f0c69c1cc6dde1fa9901befd1ac *inst/doc/DMRcaller.R
4a0c2528a481aeb420f90ef800cf2d28 *inst/doc/DMRcaller.Rmd
e25fc7feae564382c0fe2b68622d9ab8 *inst/doc/DMRcaller.html
ae51776ed063a8a5c00295c5136e040e *inst/extdata/scanBamChr1Random5.bam
6b03b55fb4d60a5afa8835a37152349d *inst/extdata/scanBamChr1Random5.bam.bai
89b64592650a37a6304bf7c227848d5a *inst/unitTests/test_DMRcaller.R
828c3e3e5177a9e325eeefaec5e44d9c *man/DMRcaller.Rd
3b130ef6ceaccd7c2856cfd863291106 *man/DMRsNoiseFilterCG.Rd
caeab8c5580fdc5acae6603a420872ac *man/GEs.Rd
ead8b69d53aab9bd2c31a926b3fad81e *man/GEs_hg38.Rd
a0d376d53704a293d4faf1b02d735d2b *man/PMDsBinsCG.Rd
9287c049a75a8d711d5a43b6d7920db2 *man/PMDsNoiseFilterCG.Rd
f69bf7f6d6050376dd0b7bb71de86961 *man/analyseReadsInsideRegionsForCondition.Rd
58087d89560f4a6569f658c1cfd072f3 *man/analyseReadsInsideRegionsForConditionPMD.Rd
c141ded0cdf0c45a008329058c7759f0 *man/computeCoMethylatedPositions.Rd
e8e66eb7dba9f2e3547e176dd61bb57a *man/computeCoMethylatedRegions.Rd
65260d27be95c8f3a25b22185b9e2680 *man/computeDMRs.Rd
10c4a15a67710cdd2cea03f626e42a26 *man/computeDMRsReplicates.Rd
c012632ed8abe2a2fff53a6432459659 *man/computeMethylationDataCoverage.Rd
b200aa82757c27ae09bb3d624c891fb7 *man/computeMethylationDataSpatialCorrelation.Rd
1decd5b14d820926a1afecb140e2e9ae *man/computeMethylationProfile.Rd
956a66ce534464b1b7f28c128192a567 *man/computeOverlapProfile.Rd
91a5ba005501393a6425404201442006 *man/computePMDs.Rd
cf50fb0ad16ff5938828c64ba1fcf12b *man/computeVMDs.Rd
756fa697ca5ce3a2f2470ad94728e029 *man/dot-analyseReadsInsideBins.Rd
ee870af14030fe4e7dbb2eff116b638b *man/dot-analyseReadsInsideBinsOneSample.Rd
e3cc517bb8af33b699451b6846c5d0d2 *man/dot-analyseReadsInsideBinsPMDs.Rd
df80159117adf02a584903b4ac85d689 *man/dot-analyseReadsInsideBinsReplicates.Rd
69dcf001c0bdf38399bffdfcbc8cdcb3 *man/dot-analyseReadsInsideRegions.Rd
a309008c376d5df85faba5e101674142 *man/dot-analyseReadsInsideRegionsForCondition.Rd
01189e1a4c272e059ef53897a8fc474c *man/dot-analyseReadsInsideRegionsOneSample.Rd
b7a808b7ed8c15f0e364df222f5c02b9 *man/dot-analyseReadsInsideRegionsPMDs.Rd
3e2b48b6ae7dcc5d1a64864c340f4a2e *man/dot-analyseReadsInsideRegionsReplicates.Rd
a67d04d83cc2a4f1310497f38ead0d12 *man/dot-analyseReadsInsideRegionsVMDs.Rd
563d5bf22d6d3b1346f49c6f345cb285 *man/dot-analyseReadsInsideRegionsVMR.Rd
81401e9188352a6b08978c2881c08410 *man/dot-chooseBPPARAM.Rd
f4040dedd3f186e84c67023304bfbd00 *man/dot-computeAdjuestedPValues.Rd
f8e812e9da1d863da7837a036abca530 *man/dot-computeAdjuestedPValuesReplicates.Rd
7f29eb99b1308227d47a318e410699c3 *man/dot-computeBetaReg.Rd
5424e7abf0e167a73c5b2780909a992a *man/dot-computeBetaRegSingle.Rd
af1853dd8c6da1c4cf0a1b3583556f2e *man/dot-computeDMRsBins.Rd
4b9a2bc1e7532c1d56b58024f14efe74 *man/dot-computeDMRsNeighbourhood.Rd
01a9d7b6be71fc90cee14b5b9fc3b5e3 *man/dot-computeDMRsNoiseFilter.Rd
988d32c4e9a9120b028350555c358fc6 *man/dot-computeDMRsReplicatesBins.Rd
57a5386a59bea61794d6f96aee3deee3 *man/dot-computeDMRsReplicatesNeighbourhood.Rd
022091efbcf3395d19657d685165aff2 *man/dot-computeMethylationDataSpatialCorrelation.Rd
49f49ff7f5c1eb769eee09581a143c16 *man/dot-computePMDsBins.Rd
61efdc006d2b5f1bf6a1df57d826979a *man/dot-computePMDsNeighbourhood.Rd
ad703fb1962dc669f7d039d4cc580be3 *man/dot-computePMDsNoiseFilter.Rd
5dcab9955c6091a836e1538f20f3a6bd *man/dot-computeProportionsInDMRs.Rd
5a62843369ddaff71c1a1fdcc99d51b3 *man/dot-computeVMDsBins.Rd
1532469aa7a4a2a7ebd71a845b2a5602 *man/dot-computeaAjustedPValuesInDMRs.Rd
c82625cfebc89fecd2e209f6ff0a08e9 *man/dot-computeaAjustedPValuesInDMRsReplicates.Rd
1733a0a996e6e58611c84ff065a0f876 *man/dot-convertResult.Rd
2ddd41bde6b725049e580e6f556c10c2 *man/dot-countCytosinesInside.Rd
1bc07b04ae50b0e6bf301ee05bc0b3c7 *man/dot-countMethylationDataCoverage.Rd
27d7c5ff7969c29fa6fd5791c60a8e80 *man/dot-countTotalNumberOfCytosines.Rd
73b3fb00db3c5216f20d66a6471f215d *man/dot-fisherTest.Rd
a79e9dc4dc00ad55a709b4d17bcb9877 *man/dot-fisherTestPValue.Rd
fde7455d21c51ecdd03d1b207a0be7fb *man/dot-isColor.Rd
b1bcca5649235b9f1cd54d7acbd7ea90 *man/dot-isInteger.Rd
2c1d30ae0c5fcb485c090bbbb632711d *man/dot-joinMethylationData.Rd
c0e11b9938d80a11d20b034e44739d5d *man/dot-mergeDMRsIteratively.Rd
a7cb1858b89b6e44a69938c461b5589d *man/dot-mergePMDsIteratively.Rd
696eadf68937cd7d3fb40c85a7e4ecdf *man/dot-movingAverage.Rd
7529a0b2462f51276f81163390ce558b *man/dot-movingSum.Rd
0b275885fdf18cea3f09133184b7da65 *man/dot-plotGeneticElements.Rd
82ddc81be4a5f727ec714d220880e4b9 *man/dot-printGenomicRanges.Rd
c500cf0181a141e07fd24ab9e2bdba5e *man/dot-scoreTest.Rd
220fa8b9a687898c0d843b95f6ffdd39 *man/dot-smartMergeDMRs.Rd
2c4203d7f2ae97f4334647488f743def *man/dot-smartMergeDMRsReplicates.Rd
d6086f373c77d316b879cd12d39d53b4 *man/dot-smartMergePMDs.Rd
89e999d614967a15fcb395aee2e62dce *man/dot-splitGRangesEqualy.Rd
2d3ba47a832b0af840576e06cfe9ab45 *man/dot-stopIfNotAll.Rd
f8e83d799a7b63cbd6ff41ca12b9f703 *man/dot-validateBPPARAM.Rd
ae8a7c4e0ede02aecb52e2c4c585d3ec *man/dot-validateBamfile.Rd
ab96cfd07722c094d489ab38c7be9b3f *man/dot-validateChromosome.Rd
1c87f33c9b842d52bcb43d28e2e488c8 *man/dot-validateCoMethylationAlternative.Rd
4d7350180f80555d423de9ef0093522e *man/dot-validateCoMethylationStatTest.Rd
0500bf5c9b7ff59cc4c46eadc39186b2 *man/dot-validateConditionReplicates.Rd
7e7822b7558af84bfc08ab3b2505de9e *man/dot-validateContext.Rd
8dbb15858921d585af577bfddf84e066 *man/dot-validateCorrelationStatTest.Rd
0e3edf47c96ae518da72cb0786b1e876 *man/dot-validateGRanges.Rd
009c35610e6926ec17c005769af1b0ec *man/dot-validateGenome.Rd
8803cc7a05fef2612267f2de63bbd47e *man/dot-validateMethylationData.Rd
cbd21b675df277b99f78e5f2901d123a *man/dot-validateMethylationDataList.Rd
f5336139287e0ef87dd716d440c0a0da *man/dot-validateMethylationProfile.Rd
7951be39e7b9206b92ba4050c992a4db *man/dot-validateModif.Rd
1ca9473dfc8e57b2f0b5e5da20dccced *man/dot-validateStatisticalTest.Rd
471996f4ad2e54e1d3a8ffd9241b4c21 *man/dot-validateStatisticalTestReplicates.Rd
8904b7d49372ea4dd7c03a0aa544c96e *man/extractGC.Rd
1268b87c90b0749541dbd42caf13e5f9 *man/filterDMRs.Rd
5f3c20bc99b2bed6040bff85e30a5cad *man/filterPMDs.Rd
d0841f6ac5e18488d5069e01801d21ba *man/filterVMDs.Rd
5327e777828075a4fbbeec66f82a3555 *man/filterVMRsONT.Rd
0078bf5dda6ffc17bd2e548436d26999 *man/getWholeChromosomes.Rd
50ddd265de1293d0d693453419e6c596 *man/joinReplicates.Rd
69727213c7eda2f3e9d69f32d4e06f01 *man/mergeDMRsIteratively.Rd
ac712d162b8d223a33e8c7706e6eb557 *man/mergePMDsIteratively.Rd
e3f5caa367e9eb61ec895395820b4059 *man/methylationDataList.Rd
0229007426919ed669a76c2ef4473fba *man/ontSampleGRangesList.Rd
82d6638e1a080a58d3c0e3c8aa1a8f0f *man/ont_gr_GM18870_chr1_PMD_bins_1k.Rd
8f87c00056cd3e839990e3b82cf6099d *man/ont_gr_GM18870_chr1_sorted_bins_1k.Rd
551519757d1298d7ec8260f43be1c942 *man/plotLocalMethylationProfile.Rd
a84f4d4006b08b76b0f7fd30a33f1b1d *man/plotMethylationDataCoverage.Rd
22a2b74ea7e1555423ac1f0c5a86bfc6 *man/plotMethylationDataSpatialCorrelation.Rd
a4a8367d98d6c5832aed8addb3937306 *man/plotMethylationProfile.Rd
5a282093fc958d1b342ca1e697a38a76 *man/plotMethylationProfileFromData.Rd
a795bdd0d30e55bb539196bdf09c5f15 *man/plotOverlapProfile.Rd
c9072bceee8f0f85107b8644c127a108 *man/poolMethylationDatasets.Rd
80a78b2c8669b067fb5115007700a3dc *man/poolTwoMethylationDatasets.Rd
abfa0d8e17eebf6df0d7f6089bad7197 *man/readBismark.Rd
c609fe282beb0e4f01bce1d6cbc0a7eb *man/readBismarkPool.Rd
e7784bd3e06d5704c54d03a8c1f32c58 *man/readONTbam.Rd
c6da46a2a26daded35943ec3630c9423 *man/saveBismark.Rd
c5231ae9d6aaaf6c2bd40eb2f1ce1de2 *man/scanBamChr1Random5.Rd
30e57458dca591a6dc70b297db1eb1b8 *man/selectCytosine.Rd
1e65f7d52d67c2843047a46fa152b07a *man/syntheticDataReplicates.Rd
eb7f44f29f77104f9f67b7737ca5947d *tests/runTests.R
4a0c2528a481aeb420f90ef800cf2d28 *vignettes/DMRcaller.Rmd
c4c91d3e4c30b44b4edd3ca3a11a2a3b *vignettes/DMRcaller.bib
0a7068e2a54ccffc75dbf8d0c4b133b8 *vignettes/apa.csl
