Package: RnBeads 2.25.0

Fabian Mueller

RnBeads: RnBeads

RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.

Authors:Yassen Assenov [aut], Christoph Bock [aut], Pavlo Lutsik [aut], Michael Scherer [aut], Fabian Mueller [aut, cre]

RnBeads_2.25.0.tar.gz
RnBeads_2.25.0.zip(r-4.5)RnBeads_2.25.0.zip(r-4.4)RnBeads_2.25.0.zip(r-4.3)
RnBeads_2.25.0.tgz(r-4.4-any)RnBeads_2.25.0.tgz(r-4.3-any)
RnBeads_2.25.0.tar.gz(r-4.5-noble)RnBeads_2.25.0.tar.gz(r-4.4-noble)
RnBeads_2.25.0.tgz(r-4.4-emscripten)RnBeads_2.25.0.tgz(r-4.3-emscripten)
RnBeads.pdf |RnBeads.html✨
RnBeads/json (API)
NEWS

# Install 'RnBeads' in R:
install.packages('RnBeads', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:RnBeads-2.25.0(bioc 3.21)RnBeads-2.24.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dnamethylationmethylationarraymethylseqepigeneticsqualitycontrolpreprocessingbatcheffectdifferentialmethylationsequencingcpgislandimmunooncologytwochanneldataimport

6.90 score 1 packages 166 scripts 720 downloads 145 mentions 258 exports 161 dependencies

Last updated 2 months agofrom:3ab7825d89. Checks:OK: 1 NOTE: 1 ERROR: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 17 2024
R-4.5-winERRORDec 17 2024
R-4.5-linuxNOTEDec 17 2024
R-4.4-winERRORDec 17 2024
R-4.4-macERRORDec 17 2024
R-4.3-winERRORDec 17 2024
R-4.3-macERRORDec 17 2024

Exports:addDiffMethTableaddPhenoaddRegionSubsegmentsannotationapply.iEVORAassemblyBMIQcombine.rnb.setscombineTestPvalsMethcomputeDiffTab.default.regioncomputeDiffTab.default.sitecomputeDiffTab.extended.sitecovgcreate.densityScattercreate.scatter.dens.pointscreateReportcreateReportGgPlotcreateReportPlotdata.frame2GRangesdestroydeviation.plot.betadiffVardownloadLolaDbsdpvalestimateProportionsCPexportDMRs2regionFileget.adjustment.variablesget.comparison.grouplabelsget.comparison.groupsizesget.comparison.infoget.comparisonsget.covariates.ctget.covariates.svaget.covg.thresget.cpg.statsget.filesget.region.typesget.site.test.methodget.tableget.variability.methodgetCellTypesFromLolaDbgetExecutablegetModuleNumCoresgetNamesFromLolaDbgetSubCmdStrgetSubCmdTokensgetTargetFromLolaDbgreedycut.filter.matrixgreedycut.get.statisticsgreedycut.get.submatrixhas.covariates.cthas.covariates.svahasCovgincludes.sitesinitializeis.validisImputedjoin.diffMethlimmaPload.region.subsegment.annotationload.rnb.diffmethload.rnb.setloadLolaDbslogger.argumentlogger.closelogger.completedlogger.errorlogger.getfileslogger.infologger.isinitializedlogger.machine.namelogger.startlogger.statuslogger.validate.filelogger.warninglolaBarPlotlolaBoxPlotPerTargetlolaVolcanoPlotMmergeSamplesmethmvalnsitesoffparallel.getNumWorkersparallel.isEnabledparallel.setupparallel.teardownperformGoEnrichment.diffMethperformGOenrichment.diffMeth.entrezperformGOEnrichment.diffVarperformLolaEnrichment.diffMethperformLolaEnrichment.diffVarphenoprepareSOFTfileForGEOqcread.bed.filesread.data.dirread.GS.reportread.idat.filesread.sample.annotationread.single.bedrefFreeEWASPregionMappingregionsreloadremove.regionsremove.samplesremove.sitesrnb.add.figurernb.add.listrnb.add.paragraphrnb.add.referencernb.add.sectionrnb.add.tablernb.add.tablesrnb.annotation.sizernb.annotation2data.framernb.bed.from.segmentationrnb.beta2mvalrnb.boxplot.from.segmentationrnb.build.indexrnb.color.legendsrnb.combine.arraysrnb.combine.seqrnb.execute.age.predictionrnb.execute.batch.qcrnb.execute.batcheffectsrnb.execute.clusteringrnb.execute.clustering.allrnb.execute.computeDiffMethrnb.execute.context.removalrnb.execute.cross.reactive.removalrnb.execute.ct.estimationrnb.execute.diffVarrnb.execute.dreductionrnb.execute.export.csvrnb.execute.filter.summaryrnb.execute.genomewidernb.execute.greedycutrnb.execute.high.coverage.removalrnb.execute.high.dpval.maskingrnb.execute.importrnb.execute.imputationrnb.execute.low.coverage.maskingrnb.execute.lumprnb.execute.na.removalrnb.execute.normalizationrnb.execute.pOOBAHrnb.execute.qualityrnb.execute.segmentationrnb.execute.sex.predictionrnb.execute.sex.removalrnb.execute.snp.removalrnb.execute.svarnb.execute.tntrnb.execute.trainingrnb.execute.variability.removalrnb.export.all.annotationrnb.export.annotationrnb.export.to.ewasherrnb.export.to.trackhubrnb.find.relative.site.coordrnb.get.annotationrnb.get.assembliesrnb.get.chromosomesrnb.get.directoryrnb.get.mappingrnb.get.referencernb.get.reliability.matrixrnb.getOptionrnb.infinium.control.targetsrnb.initialize.reportsrnb.is.optionrnb.load.annotationrnb.load.annotation.from.dbrnb.load.sitelistrnb.message.plotrnb.mval2betarnb.optionsrnb.options2xmlrnb.performance.profilernb.plot.beta.comparisonrnb.plot.betadistribution.probeCategoriesrnb.plot.betadistribution.sampleGroupsrnb.plot.biseq.coveragernb.plot.biseq.coverage.histrnb.plot.biseq.coverage.violinrnb.plot.control.barplotrnb.plot.control.boxplotrnb.plot.coverage.thresholdsrnb.plot.ct.heatmaprnb.plot.dreductionrnb.plot.locus.profilernb.plot.marker.fstatrnb.plot.negative.boxplotrnb.plot.num.sites.covgrnb.plot.nv.heatmaprnb.plot.pheno.categoriesrnb.plot.region.profile.densityrnb.plot.region.profilesrnb.plot.region.site.densityrnb.plot.sentrix.distributionrnb.plot.sentrix.distributionsrnb.plot.snp.barplotrnb.plot.snp.boxplotrnb.plot.snp.heatmaprnb.read.geornb.region.typesrnb.region.types.for.analysisrnb.remove.annotationrnb.RnBSet.to.bedrnb.RnBSet.to.bedGraphrnb.RnBSet.to.GRangesListrnb.run.analysisrnb.run.differentialrnb.run.djrnb.run.examplernb.run.exploratoryrnb.run.importrnb.run.inferencernb.run.preprocessingrnb.run.qcrnb.run.tntrnb.run.xmlrnb.sample.groupsrnb.sample.replicatesrnb.sample.summary.tablernb.save.annotationrnb.set.annotationrnb.set.annotation.and.cpg.statsrnb.show.reportrnb.step.betadistributionrnb.step.cnvrnb.write.tablernb.xml2optionsRnBeadRawSetRnBeadSetRnBiseqSetrowOneSampleTProwPairedTProwWelchPrunrun.cross.validationsave.rnb.diffmethsave.rnb.setsave.tablesset.covariates.ctset.covariates.svasetExecutablesetModuleNumCoressetModuleResourceRequirementssitessummarize.regionssummarized.regionsUupdateMethylationSitesupdateRegionSummaries

Dependencies:abindannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemcaToolsclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdoRNGdotCall64dplyrfansifarverfastmapFDb.InfiniumMethylation.hg19fffieldsforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegplotsgridExtragtablegtoolsHDF5Arrayhmshttrhttr2illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrmapsMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimulttestmunsellnlmenor1mixopensslorg.Hs.eg.dbpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscalesscrimeselectrsiggenessnowspamSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryamlzlibbioc

Comprehensive DNA Methylation Analysis with RnBeads

Rendered fromRnBeads.Rnwusingutils::Sweaveon Dec 17 2024.

Last update: 2023-01-03
Started: 2015-04-09

RnBeads Annotation

Rendered fromRnBeads_Annotations.Rnwusingutils::Sweaveon Dec 17 2024.

Last update: 2021-07-18
Started: 2015-04-09

Readme and manuals

Help Manual

Help pageTopics
Extract parts of BigFfMat[,BigFfMat,ANY,ANY,ANY-method
Replace parts of BigFfMat[<-,BigFfMat,ANY,ANY,ANY-method
RnBeads option values and restrictionsaccepted current infos previous
addDiffMethTable-methodsaddDiffMethTable addDiffMethTable,RnBDiffMeth-method
addPhenoaddPheno addPheno,RnBSet-method
addRegionSubsegmentsaddRegionSubsegments
annotation-methodsannotation annotation,RnBSet-method
apply.iEVORAapply.iEVORA
Conversion to/from RnBeadRawSetas.RnBeadRawSet
assembly-methodsassembly assembly,RnBSet-method
auto.select.rank.cutauto.select.rank.cut
BMIQBMIQ
ClusterArchitecture ClassClusterArchitecture-class
ClusterArchitectureLSF ClassClusterArchitectureLSF-class
ClusterArchitectureSGE ClassClusterArchitectureSGE-class
ClusterArchitectureSLURM ClassClusterArchitectureSLURM-class
as("RnBeadSet", "MethyLumiSet")coercion-methods
cols.to.rank.sitecols.to.rank.region cols.to.rank.site
combine.diffMeth.objscombine.diffMeth.objs
combine.rnb.sets-methodscombine.rnb.sets combine.rnb.sets,RnBSet,RnBSet-method combine.rnb.sets,RnBSet-method
combineTestPvalsMethcombineTestPvalsMeth
computeDiffTab.regioncomputeDiffTab.default.region computeDiffTab.region
computeDiffTab.sitecomputeDiffTab.default.site computeDiffTab.extended.site computeDiffTab.site
covg-methodscovg covg,RnBSet-method
create.densityScattercreate.densityScatter
create.hex.summary.plotcreate.hex.summary.plot
create.scatter.dens.pointscreate.scatter.dens.points
createReportcreateReport
createReportGgPlotcreateReportGgPlot
createReportPlotcreateReportPlot
data.frame2GRangesdata.frame2GRanges
densRanksdensRanks
destroy-methodsdestroy,RnBDiffMeth-method
destroy-methodsdestroy destroy,RnBeadRawSet-method destroy,RnBeadSet-method destroy,RnBSet-method
deviation.plot.betadeviation.plot.beta
diffVardiffVar
Dimensions of BigFfMatdim,BigFfMat-method
downloadLolaDbsdownloadLolaDbs
dpval-methodsdpval dpval,RnBeadSet-method
estimateProportionsCPestimateProportionsCP
exportDMRs2regionFileexportDMRs2regionFile
get.adjustment.variablesget.adjustment.variables
get.comparison.grouplabels-methodsget.comparison.grouplabels get.comparison.grouplabels,RnBDiffMeth-method
get.comparison.groupsizes-methodsget.comparison.groupsizes get.comparison.groupsizes,RnBDiffMeth-method
get.comparison.infoget.comparison.info
get.comparisons-methodsget.comparisons get.comparisons,RnBDiffMeth-method
get.covariates.ctget.covariates.ct
get.covariates.svaget.covariates.sva
get.covg.thres-methodsget.covg.thres get.covg.thres,RnBDiffMeth-method
get.cpg.statsget.cpg.stats
get.filesget.files
get.region.types-methodsget.region.types get.region.types,RnBDiffMeth-method
get.site.test.method-methodsget.site.test.method get.site.test.method,RnBDiffMeth-method
get.table-methodsget.table get.table,RnBDiffMeth-method
Returns the colum names of the differential variability table.get.table.ids
get.variability.method-methodsget.variability.method get.variability.method,RnBDiffMeth-method
getCellTypesFromLolaDbgetCellTypesFromLolaDb
getExecutable-methodsgetExecutable getExecutable,ClusterArchitecture,character-method getExecutable,ClusterArchitecture-method
getModuleNumCores-methodsgetModuleNumCores getModuleNumCores,RnBClusterRun-method
getNamesFromLolaDbgetNamesFromLolaDb
getNumNaMeth-methodsgetNumNaMeth getNumNaMeth,RnBSet-method
getSubCmdStr-methodsgetSubCmdStr getSubCmdStr,ClusterArchitecture-method
getSubCmdTokens-methodsgetSubCmdTokens getSubCmdTokens,ClusterArchitecture-method
getSubCmdTokens-methodsgetSubCmdTokens,ClusterArchitectureLSF-method
getSubCmdTokens-methodsgetSubCmdTokens,ClusterArchitectureSGE-method
getSubCmdTokens-methodsgetSubCmdTokens,ClusterArchitectureSLURM-method
getTargetFromLolaDbgetTargetFromLolaDb
greedycut.filter.matrixgreedycut.filter.matrix
greedycut.get.statisticsgreedycut.get.statistics
greedycut.get.submatrixgreedycut.get.submatrix
has.covariates.cthas.covariates.ct
has.covariates.svahas.covariates.sva
hasCovg-methodshasCovg hasCovg,RnBSet-method
includes.sites-methodsincludes.sites includes.sites,RnBDiffMeth-method
initialize.ClusterArchitectureinitialize,ClusterArchitecture-method
initialize.ClusterArchitectureLSFinitialize,ClusterArchitectureLSF-method
initialize.ClusterArchitectureSGEinitialize,ClusterArchitectureSGE-method
initialize.ClusterArchitectureSLURMinitialize,ClusterArchitectureSLURM-method
initialize.RnBClusterRuninitialize,RnBClusterRun-method
initialize.RnBDiffMethinitialize,RnBDiffMeth-method
intensities.by.colorintensities.by.color
is.valid-methodsis.valid is.valid,RnBDiffMeth-method
isImputedisImputed isImputed,RnBSet-method
join.diffMeth-methodsjoin.diffMeth join.diffMeth,RnBDiffMeth,RnBDiffMeth-method
limmaPlimmaP
load.region.subsegment.annotationload.region.subsegment.annotation
load.rnb.diffmethload.rnb.diffmeth
load.rnb.setload.rnb.set
loadLolaDbsloadLolaDbs
logger.argumentlogger.argument
logger.getfileslogger.getfiles
logger.isinitializedlogger.isinitialized
logger.machine.namelogger.machine.name
Log File Managementlogger.close logger.completed logger.start
Writing text messages to the log file.logger.error logger.info logger.status logger.warning
logger.validate.filelogger.validate.file
lolaBarPlotlolaBarPlot
lolaBoxPlotPerTargetlolaBoxPlotPerTarget
lolaVolcanoPlotlolaVolcanoPlot
LUMP Supportlump.hg19
LUMP Support (hg38)lump.hg38
M-methodsM M,RnBeadRawSet-method
mask.sites.meth-methodsmask.sites.meth mask.sites.meth,RnBSet-method
mergeSamplesmergeSamples mergeSamples,RnBSet-method
meth-methodsmeth meth,RnBSet-method
mval-methodsmval mval,RnBSet-method
nsites-methodsnsites nsites,RnBSet-method
off-methodsoff off,Report-method off,ReportGgPlot-method off,ReportPlot-method
parallel.getNumWorkersparallel.getNumWorkers
parallel.isEnabledparallel.isEnabled
parallel.setupparallel.setup
parallel.teardownparallel.teardown
performGoEnrichment.diffMethperformGoEnrichment.diffMeth
performGOenrichment.diffMeth.entrezperformGOenrichment.diffMeth.entrez
performGOEnrichment.diffVarperformGOEnrichment.diffVar
performLolaEnrichment.diffMethperformLolaEnrichment.diffMeth
performLolaEnrichment.diffVarperformLolaEnrichment.diffVar
pheno-methodspheno pheno,RnBSet-method
prepareSOFTfileForGEOprepareSOFTfileForGEO
qc-methodsqc qc,RnBeadSet-method
read.bed.filesread.bed.files
read.data.dirread.data.dir
read.GS.reportread.GS.report
read.idat.filesread.idat.files
read.idat.files2read.idat.files2
read.sample.annotationread.sample.annotation
read.single.bedread.single.bed
refFreeEWASPrefFreeEWASP
regionMapping-methodsregionMapping regionMapping,RnBSet-method
regions-methodsregions regions,RnBSet-method
reload-methodsreload reload,RnBDiffMeth-method
remove.regions-methodsremove.regions remove.regions,RnBSet-method
remove.samples-methodsremove.samples remove.samples,RnBeadRawSet-method remove.samples,RnBeadSet-method remove.samples,RnBSet-method
remove.sites-methodsremove.sites remove.sites,RnBeadRawSet-method remove.sites,RnBeadSet-method remove.sites,RnBSet-method
Report Classinitialize,Report-method Report-class
ReportGgPlot Classinitialize,ReportGgPlot-method ReportGgPlot-class
ReportPlot Classinitialize,ReportPlot-method ReportPlot-class
rnb.add.figurernb.add.figure
rnb.add.listrnb.add.list
rnb.add.paragraphrnb.add.paragraph
rnb.add.referencernb.add.reference
rnb.add.sectionrnb.add.section
rnb.add.tablernb.add.table
rnb.add.tablesrnb.add.tables
rnb.annotation.sizernb.annotation.size
rnb.annotation2data.framernb.annotation2data.frame
rnb.bed.from.segmentationrnb.bed.from.segmentation
rnb.beta2mvalrnb.beta2mval
rnb.boxplot.from.segmentationrnb.boxplot.from.segmentation
rnb.build.indexrnb.build.index
rnb.call.destructorrnb.call.destructor
rnb.color.legendsrnb.color.legends
Combine array-based datasetsrnb.combine.arrays
rnb.combine.seqrnb.combine.seq
rnb.execute.age.predictionrnb.execute.age.prediction
rnb.execute.batch.qcrnb.execute.batch.qc
rnb.execute.batcheffectsrnb.execute.batcheffects
rnb.execute.clusteringrnb.execute.clustering
rnb.execute.clustering.allrnb.execute.clustering.all
rnb.execute.computeDiffMethrnb.execute.computeDiffMeth
rnb.execute.context.removalrnb.execute.context.removal
rnb.execute.cross.reactive.removalrnb.execute.cross.reactive.removal
rnb.execute.ct.estimationrnb.execute.ct.estimation
rnb.execute.diffVarrnb.execute.diffVar
rnb.execute.dreductionrnb.execute.dreduction
rnb.execute.export.csvrnb.execute.export.csv
rnb.execute.filter.summaryrnb.execute.filter.summary
rnb.execute.gender.predictionrnb.execute.gender.prediction
Genome-wide methylation levelrnb.execute.genomewide
rnb.execute.greedycutrnb.execute.greedycut
rnb.execute.high.coverage.removalrnb.execute.high.coverage.removal
rnb.execute.high.dpval.maskingrnb.execute.high.dpval.masking
rnb.execute.importrnb.execute.import
rnb.execute.imputationrnb.execute.imputation
rnb.execute.low.coverage.maskingrnb.execute.low.coverage.masking
Leukocytes unmethylation for purityrnb.execute.lump
rnb.execute.na.removalrnb.execute.na.removal
rnb.execute.normalizationrnb.execute.normalization
rnb.execute.pOOBAHrnb.execute.pOOBAH
rnb.execute.qualityrnb.execute.quality
rnb.execute.segmentationrnb.execute.segmentation
rnb.execute.sex.predictionrnb.execute.sex.prediction
rnb.execute.sex.removalrnb.execute.sex.removal
rnb.execute.snp.removalrnb.execute.snp.removal
rnb.execute.svarnb.execute.sva
rnb.execute.tntrnb.execute.tnt
rnb.execute.trainingrnb.execute.training
rnb.execute.variability.removalrnb.execute.variability.removal
rnb.export.all.annotationrnb.export.all.annotation
rnb.export.annotationrnb.export.annotation
rnb.export.to.ewasherrnb.export.to.ewasher
rnb.export.to.trackhubrnb.export.to.trackhub
rnb.find.relative.site.coordrnb.find.relative.site.coord
rnb.get.annotationrnb.get.annotation
rnb.get.assembliesrnb.get.assemblies
rnb.get.chromosomesrnb.get.chromosomes
rnb.get.directoryrnb.get.directory
rnb.get.mappingrnb.get.mapping
rnb.get.referencernb.get.reference
rnb.get.reliability.matrixrnb.get.reliability.matrix
rnb.infinium.control.targetsrnb.infinium.control.targets
rnb.initialize.reportsrnb.initialize.reports
rnb.is.optionrnb.is.option
rnb.load.annotationrnb.load.annotation
rnb.load.annotation.from.dbrnb.load.annotation.from.db
rnb.load.sitelistrnb.load.sitelist
rnb.message.plotrnb.message.plot
rnb.mval2betarnb.mval2beta
RnBeads Optionsrnb.getOption rnb.options
rnb.options2xmlrnb.options2xml
rnb.performance.profilernb.performance.profile
rnb.plot.beta.comparisonrnb.plot.beta.comparison
rnb.plot.betadistribution.probeCategoriesrnb.plot.betadistribution.probeCategories
rnb.plot.betadistribution.sampleGroupsrnb.plot.betadistribution.sampleGroups
rnb.plot.biseq.coveragernb.plot.biseq.coverage
rnb.plot.biseq.coverage.histrnb.plot.biseq.coverage.hist
rnb.plot.biseq.coverage.violinrnb.plot.biseq.coverage.violin
rnb.plot.control.barplotrnb.plot.control.barplot
rnb.plot.control.boxplotrnb.plot.control.boxplot
rnb.plot.coverage.thresholdsrnb.plot.coverage.thresholds
rnb.plot.ct.heatmaprnb.plot.ct.heatmap
rnb.plot.dreductionrnb.plot.dreduction
rnb.plot.locus.profilernb.plot.locus.profile
rnb.plot.marker.fstatrnb.plot.marker.fstat
rnb.plot.negative.boxplotrnb.plot.negative.boxplot
rnb.plot.num.sites.covgrnb.plot.num.sites.covg
rnb.plot.nv.heatmaprnb.plot.nv.heatmap
rnb.plot.pheno.categoriesrnb.plot.pheno.categories
rnb.plot.region.profilesrnb.plot.region.profile.density
rnb.plot.region.profilesrnb.plot.region.profiles
rnb.plot.region.site.densityrnb.plot.region.site.density
rnb.plot.sentrix.distributionrnb.plot.sentrix.distribution
rnb.plot.sentrix.distributionsrnb.plot.sentrix.distributions
rnb.plot.snp.barplotrnb.plot.snp.barplot
rnb.plot.snp.boxplotrnb.plot.snp.boxplot
rnb.plot.snp.heatmaprnb.plot.snp.heatmap
Import methylation data from GEOrnb.read.geo
rnb.region.typesrnb.region.types
rnb.region.types.for.analysisrnb.region.types.for.analysis
rnb.remove.annotationrnb.remove.annotation
Export to BED filesrnb.RnBSet.to.bed
rnb.RnBSet.to.bedGraphrnb.RnBSet.to.bedGraph
rnb.RnBSet.to.GRangesListrnb.RnBSet.to.GRangesList
RnBeads Analysis Pipelinernb.run.analysis
rnb.run.djrnb.run.dj
rnb.run.examplernb.run.example
RnBeads Modules in the Analysis Pipelinernb.run.differential rnb.run.exploratory rnb.run.import rnb.run.inference rnb.run.preprocessing rnb.run.qc rnb.run.tnt
rnb.run.xmlrnb.run.xml
rnb.sample.groupsrnb.sample.groups
rnb.sample.replicatesrnb.sample.replicates
rnb.sample.summary.tablernb.sample.summary.table rnb.sample.summary.table,RnBSet-method
rnb.save.annotationrnb.save.annotation
rnb.section.diffVar.regionrnb.section.diffVar.region
rnb.set.annotationrnb.set.annotation
rnb.set.annotation.and.cpg.statsrnb.set.annotation.and.cpg.stats
rnb.show.reportrnb.show.report
rnb.step.betadistributionrnb.step.betadistribution
rnb.step.cnvrnb.step.cnv
rnb.write.tablernb.write.table
rnb.xml2optionsrnb.xml2options
RnBClusterRun ClassRnBClusterRun-class
RnBDiffMeth ClassRnBDiffMeth-class
RnBeadClustering Classinitialize,RnBeadClustering-method RnBeadClustering-class
RnBeadRawSet-classinitialize,RnBeadRawSet-method RnBeadRawSet RnBeadRawSet-class
Analysis of genome-scale DNA methylation data with RnBeadsRnBeads-package RnBeads
RnBeads Annotation TablesRnBeads.data
RnBeadSet Classinitialize,RnBeadSet-method RnBeadSet RnBeadSet-class
RnBiseqSet Classinitialize,RnBiseqSet-method RnBiseqSet RnBiseqSet-class
RnBSet ClassRnBSet-class
rowOneSampleTProwOneSampleTP
rowPairedTProwPairedTP
rowWelchProwWelchP
run-methodsrun run,RnBClusterRun-method
run.cross.validationrun.cross.validation
sampleCovgApply-methodssampleCovgApply sampleCovgApply,RnBSet-method
sampleMethApply-methodssampleMethApply sampleMethApply,RnBSet-method
samples-methodssamples samples,RnBeadClustering-method samples,RnBSet-method
save.rnb.diffmethsave.rnb.diffmeth
save.rnb.setsave.rnb.set
save.tables-methodssave.tables save.tables,RnBDiffMeth-method
set.covariates.ctset.covariates.ct
set.covariates.svaset.covariates.sva
setExecutable-methodssetExecutable setExecutable,ClusterArchitecture,character,character-method setExecutable,ClusterArchitecture-method
setModuleNumCores-methodssetModuleNumCores setModuleNumCores,RnBClusterRun,integer,character-method setModuleNumCores,RnBClusterRun-method
setModuleResourceRequirements-methodssetModuleResourceRequirements setModuleResourceRequirements,RnBClusterRun,character,character-method setModuleResourceRequirements,RnBClusterRun-method
sites-methodssites sites,RnBSet-method
summarize.regions-methodssummarize.regions summarize.regions,RnBSet-method
summarized.regions-methodssummarized.regions summarized.regions,RnBSet-method
U-methodsU U,RnBeadRawSet-method
updateMethylationSites-methodsupdateMethylationSites updateMethylationSites,RnBSet-method
updateRegionSummariesupdateRegionSummaries updateRegionSummaries,RnBSet-method