Files in methylKit

DNA methylation analysis from high-throughput bisulfite sequencing results

README.md R/RcppExports.R R/dataSim.R R/methylKit.R R/regionalize.R R/deprecated_defunct.R R/backbone.R R/batchControl.R R/adjustMethylC.R R/updateMethObject.R R/diffMethDSS.R R/reorganize.R R/clusterSamples.R R/methSeg.R R/methylDBFunctions.R R/percMethylation.R R/processBismarkAln.R R/bedgraph.R R/onUnload.R R/normalizeCoverage.R R/diffMeth.R R/methylDBClasses.R R/pool.R R/document_data.R R/tabix.functions.R inst/doc/methylKit.R inst/doc/methylKit.Rmd inst/scripts/create.data.R tests/testthat.R tests/testthat/test-19-getCoverageStats.r tests/testthat/test-reorganize.R tests/testthat/test-20-normalizeCoverage.r tests/testthat/test-3-clusterSamples.r tests/testthat/test-16-loadTabix.r tests/testthat/test-batchControl.R tests/testthat/test-methRead_addon.R tests/testthat/test-10-readTabix.r tests/testthat/test-999-tidyUp.r tests/testthat/test-14-methRawListConstructor.r tests/testthat/test-diffMethPerChr.R tests/testthat/test-8-calculateDiffMethDSS.r tests/testthat/test-17-bedgraph.r tests/testthat/test-8-methSeg.r tests/testthat/test-11-pool.r tests/testthat/test-13-applyTbxByOverlap.r tests/testthat/test-unite_addon.r tests/testthat/test-6-regionCounts.r tests/testthat/test-15-adjustMethylC.R tests/testthat/test-percMethylation.R tests/testthat/test-5-processBismarkAln.r tests/testthat/test-2-unite.r tests/testthat/test-18-getMethylationStats.r tests/testthat/test-4-calculateDiffMeth.r tests/testthat/test-12-selectByOverlap.r tests/testthat/test-getMethylDiff.R tests/testthat/test-1-methRead.r tests/testthat/test-7-dataSim.r vignettes/methylKit.Rmd man/getCorrelation-methods.Rd man/reconstruct-methods.Rd man/dataSim-methods.Rd man/calculateDiffMeth-methods.Rd man/getContext-methods.Rd man/methylBaseDB-class.Rd man/removeComp-methods.Rd man/reorganize-methods.Rd man/methylDiff-class.Rd man/pool-methods.Rd man/getTreatment-methods.Rd man/PCASamples-methods.Rd man/getDBPath-methods.Rd man/methylKit-defunct.Rd man/select-methods.Rd man/tileMethylCounts-methods.Rd man/methSeg.Rd man/regionCounts.Rd man/methSeg2bed.Rd man/getSampleID-methods.Rd man/getData-methods.Rd man/methylRawDB-class.Rd man/unite-methods.Rd man/makeMethylDB-methods.Rd man/assocComp-methods.Rd man/methylRawListDB-class.Rd man/joinSegmentNeighbours.Rd man/bedgraph-methods.Rd man/getCoverageStats-methods.Rd man/methylDiff.obj.Rd man/diffMethPerChr-methods.Rd man/percMethylation-methods.Rd man/readMethylDB-methods.Rd man/processBismarkAln-methods.Rd man/calculateDiffMethDSS-methods.Rd man/updateMethObject.Rd man/clusterSamples-methods.Rd man/getMethylationStats-methods.Rd man/methylRawList-class.Rd man/methRead-methods.Rd man/normalizeCoverage-methods.Rd man/methylDiffDB-class.Rd man/getAssembly-methods.Rd man/filterByCoverage-methods.Rd man/methylRawList.obj.Rd man/show-methods.Rd man/selectByOverlap-methods.Rd man/methylRaw-class.Rd man/extract-methods.Rd man/adjustMethylC.Rd man/methylBase.obj.Rd man/getMethylDiff-methods.Rd man/methylBase-class.Rd