BMIQ                    BMIQ
ClusterArchitecture-class
                        ClusterArchitecture Class
ClusterArchitectureSGE-class
                        ClusterArchitectureSGE Class
M,RnBeadRawSet-method   M-methods
Report-class            Report Class
ReportGgPlot-class      ReportGgPlot Class
ReportPlot-class        ReportPlot Class
RnBClusterRun-class     RnBClusterRun Class
RnBDiffMeth-class       RnBDiffMeth Class
RnBSet-class            RnBSet Class
RnBeadClustering-class
                        RnBeadClustering Class
RnBeadRawSet-class      RnBeadRawSet-class
RnBeadSet-class         RnBeadSet Class
RnBeads                 Analysis of genome-scale DNA methylation data
                        with RnBeads
RnBeads.data            RnBeads Annotation Tables
RnBiseqSet-class        RnBiseqSet Class
U,RnBeadRawSet-method   U-methods
[,BigFfMat,ANY,ANY,ANY-method
                        Extract parts of BigFfMat
[<-,BigFfMat,ANY,ANY,ANY-method
                        Replace parts of BigFfMat
accepted                RnBeads option values and restrictions
addDiffMethTable,RnBDiffMeth-method
                        addDiffMethTable-methods
addPheno,RnBSet-method
                        addPheno
addRegionSubsegments    addRegionSubsegments
annotation,RnBSet-method
                        annotation-methods
as.RnBeadRawSet         Conversion to/from RnBeadRawSet
assembly,RnBSet-method
                        assembly-methods
auto.select.rank.cut    auto.select.rank.cut
coercion-methods        as("RnBeadSet", "MethyLumiSet")
combine,RnBSet,RnBSet-method
                        combine-methods
combine.diffMeth.objs   combine.diffMeth.objs
combineTestPvalsMeth    combineTestPvalsMeth
computeDiffTab.default.region
                        computeDiffTab.region
computeDiffTab.default.site
                        computeDiffTab.site
covg,RnBSet-method      covg-methods
create.densityScatter   create.densityScatter
create.hex.summary.plot
                        create.hex.summary.plot
create.scatter.dens.points
                        create.scatter.dens.points
createReport            createReport
createReportGgPlot      createReportGgPlot
createReportPlot        createReportPlot
data.frame2GRanges      data.frame2GRanges
densRanks               densRanks
destroy,RnBDiffMeth-method
                        destroy-methods
destroy,RnBSet-method   destroy-methods
deviation.plot.beta     deviation.plot.beta
dim,BigFfMat-method     Dimensions of BigFfMat
dpval,RnBeadSet-method
                        dpval-methods
estimateProportionsCP   estimateProportionsCP
exportDMRs2regionFile   exportDMRs2regionFile
get.adjustment.variables
                        get.adjustment.variables
get.comparison.grouplabels,RnBDiffMeth-method
                        get.comparison.grouplabels-methods
get.comparison.groupsizes,RnBDiffMeth-method
                        get.comparison.groupsizes-methods
get.comparison.info     get.comparison.info
get.comparisons,RnBDiffMeth-method
                        get.comparisons-methods
get.covariates.ct       get.covariates.ct
get.covariates.sva      get.covariates.sva
get.covg.thres,RnBDiffMeth-method
                        get.covg.thres-methods
get.cpg.stats           get.cpg.stats
get.files               get.files
get.region.types,RnBDiffMeth-method
                        get.region.types-methods
get.site.test.method,RnBDiffMeth-method
                        get.site.test.method-methods
get.table,RnBDiffMeth-method
                        get.table-methods
getExecutable,ClusterArchitecture,character-method
                        getExecutable-methods
getModuleNumCores,RnBClusterRun-method
                        getModuleNumCores-methods
getNumNaMeth,RnBSet-method
                        getNumNaMeth-methods
getSubCmdStr,ClusterArchitecture-method
                        getSubCmdStr-methods
getSubCmdTokens,ClusterArchitecture-method
                        getSubCmdTokens-methods
getSubCmdTokens,ClusterArchitectureSGE-method
                        getSubCmdTokens-methods
greedycut.filter.matrix
                        greedycut.filter.matrix
greedycut.get.statistics
                        greedycut.get.statistics
greedycut.get.submatrix
                        greedycut.get.submatrix
has.covariates.ct       has.covariates.ct
has.covariates.sva      has.covariates.sva
hasCovg,RnBSet-method   hasCovg-methods
includes.sites,RnBDiffMeth-method
                        includes.sites-methods
initialize,ClusterArchitecture-method
                        initialize.ClusterArchitecture
initialize,ClusterArchitectureSGE-method
                        initialize.ClusterArchitectureSGE
initialize,RnBClusterRun-method
                        initialize.RnBClusterRun
initialize,RnBDiffMeth-method
                        initialize.RnBDiffMeth
intensities.by.color    intensities.by.color
is.valid,RnBDiffMeth-method
                        is.valid-methods
join.diffMeth,RnBDiffMeth,RnBDiffMeth-method
                        join.diffMeth-methods
limmaP                  limmaP
load.region.subsegment.annotation
                        load.region.subsegment.annotation
load.rnb.diffmeth       load.rnb.diffmeth
load.rnb.set            load.rnb.set
logger.argument         logger.argument
logger.getfiles         logger.getfiles
logger.isinitialized    logger.isinitialized
logger.machine.name     logger.machine.name
logger.start            Log File Management
logger.status           Writing text messages to the log file.
logger.validate.file    logger.validate.file
mask.sites.meth,RnBSet-method
                        mask.sites.meth-methods
mergeSamples,RnBSet-method
                        mergeSamples
meth,RnBSet-method      meth-methods
mval,RnBSet-method      mval-methods
nsites,RnBSet-method    nsites-methods
off,Report-method       off-methods
parallel.getNumWorkers
                        parallel.getNumWorkers
parallel.isEnabled      parallel.isEnabled
parallel.setup          parallel.setup
parallel.teardown       parallel.teardown
performEnrichment.diffMeth
                        performEnrichment.diffMeth
performGOenrichment.diffMeth.entrez
                        performGOenrichment.diffMeth.entrez
pheno,RnBSet-method     pheno-methods
qc,RnBeadSet-method     qc-methods
read.GS.report          read.GS.report
read.bed.files          read.bed.files
read.data.dir           read.data.dir
read.geo                read.geo
read.geo.parse.characteristics_ch1
                        read.geo.parse.characteristics_ch1
read.idat.files         read.idat.files
read.idat.files2        read.idat.files2
read.sample.annotation
                        read.sample.annotation
read.single.bed         read.single.bed
refFreeEWASP            refFreeEWASP
regionMapping,RnBSet-method
                        regionMapping-methods
regions,RnBSet-method   regions-methods
reload,RnBDiffMeth-method
                        reload-methods
remove.regions,RnBSet-method
                        remove.regions-methods
remove.samples,RnBSet-method
                        remove.samples-methods
remove.sites,RnBSet-method
                        remove.sites-methods
rnb.RnBSet.to.GRangesList
                        rnb.RnBSet.to.GRangesList
rnb.RnBSet.to.bed       Export to BED files
rnb.RnBSet.to.bedGraph
                        rnb.RnBSet.to.bedGraph
rnb.add.figure          rnb.add.figure
rnb.add.list            rnb.add.list
rnb.add.paragraph       rnb.add.paragraph
rnb.add.reference       rnb.add.reference
rnb.add.section         rnb.add.section
rnb.add.table           rnb.add.table
rnb.add.tables          rnb.add.tables
rnb.annotation.size     rnb.annotation.size
rnb.annotation2data.frame
                        rnb.annotation2data.frame
rnb.beta2mval           rnb.beta2mval
rnb.build.index         rnb.build.index
rnb.call.destructor     rnb.call.destructor
rnb.color.legends       rnb.color.legends
rnb.execute.age.prediction
                        rnb.execute.age.prediction
rnb.execute.batch.qc    rnb.execute.batch.qc
rnb.execute.batcheffects
                        rnb.execute.batcheffects
rnb.execute.clustering
                        rnb.execute.clustering
rnb.execute.clustering.all
                        rnb.execute.clustering.all
rnb.execute.computeDiffMeth
                        rnb.execute.computeDiffMeth
rnb.execute.context.removal
                        rnb.execute.context.removal
rnb.execute.cross.reactive.removal
                        rnb.execute.cross.reactive.removal
rnb.execute.ct.estimation
                        rnb.execute.ct.estimation
rnb.execute.dreduction
                        rnb.execute.dreduction
rnb.execute.export.csv
                        rnb.execute.export.csv
rnb.execute.filter.summary
                        rnb.execute.filter.summary
rnb.execute.gender.prediction
                        rnb.execute.gender.prediction
rnb.execute.greedycut   rnb.execute.greedycut
rnb.execute.high.coverage.removal
                        rnb.execute.high.coverage.removal
rnb.execute.import      rnb.execute.import
rnb.execute.low.coverage.masking
                        rnb.execute.low.coverage.masking
rnb.execute.na.removal
                        rnb.execute.na.removal
rnb.execute.normalization
                        rnb.execute.normalization
rnb.execute.quality     rnb.execute.quality
rnb.execute.sex.removal
                        rnb.execute.sex.removal
rnb.execute.snp.removal
                        rnb.execute.snp.removal
rnb.execute.sva         rnb.execute.sva
rnb.execute.tnt         rnb.execute.tnt
rnb.execute.training    rnb.execute.age.training
rnb.execute.variability.removal
                        rnb.execute.variability.removal
rnb.export.all.annotation
                        rnb.export.all.annotation
rnb.export.annotation   rnb.export.annotation
rnb.export.to.ewasher   rnb.export.to.ewasher
rnb.export.to.trackhub
                        rnb.export.to.trackhub
rnb.find.relative.site.coord
                        rnb.find.relative.site.coord
rnb.get.annotation      rnb.get.annotation
rnb.get.assemblies      rnb.get.assemblies
rnb.get.chromosomes     rnb.get.chromosomes
rnb.get.directory       rnb.get.directory
rnb.get.mapping         rnb.get.mapping
rnb.get.reference       rnb.get.reference
rnb.get.reliability.matrix
                        rnb.get.reliability.matrix
rnb.infinium.control.targets
                        rnb.infinium.control.targets
rnb.initialize.reports
                        rnb.initialize.reports
rnb.is.option           rnb.is.option
rnb.load.annotation     rnb.load.annotation
rnb.load.sitelist       rnb.load.sitelist
rnb.message.plot        rnb.message.plot
rnb.mval2beta           rnb.mval2beta
rnb.options             RnBeads Options
rnb.options2xml         rnb.options2xml
rnb.performance.profile
                        rnb.performance.profile
rnb.plot.beta.comparison
                        rnb.plot.beta.comparison
rnb.plot.betadistribution.probeCategories
                        rnb.plot.betadistribution.probeCategories
rnb.plot.betadistribution.sampleGroups
                        rnb.plot.betadistribution.sampleGroups
rnb.plot.biseq.coverage
                        rnb.plot.biseq.coverage
rnb.plot.biseq.coverage.hist
                        rnb.plot.biseq.coverage.hist
rnb.plot.biseq.coverage.violin
                        rnb.plot.biseq.coverage.violin
rnb.plot.control.barplot
                        rnb.plot.control.barplot
rnb.plot.control.boxplot
                        rnb.plot.control.boxplot
rnb.plot.coverage.thresholds
                        rnb.plot.coverage.thresholds
rnb.plot.ct.heatmap     rnb.plot.ct.heatmap
rnb.plot.dreduction     rnb.plot.dreduction
rnb.plot.locus.profile
                        rnb.plot.locus.profile
rnb.plot.marker.fstat   rnb.plot.marker.fstat
rnb.plot.negative.boxplot
                        rnb.plot.negative.boxplot
rnb.plot.num.sites.covg
                        rnb.plot.num.sites.covg
rnb.plot.pheno.categories
                        rnb.plot.pheno.categories
rnb.plot.region.profile.density
                        rnb.plot.region.profiles
rnb.plot.region.profiles
                        rnb.plot.region.profiles
rnb.plot.region.site.density
                        rnb.plot.region.site.density
rnb.plot.sentrix.distribution
                        rnb.plot.sentrix.distribution
rnb.plot.sentrix.distributions
                        rnb.plot.sentrix.distributions
rnb.plot.snp.barplot    rnb.plot.snp.barplot
rnb.plot.snp.boxplot    rnb.plot.snp.boxplot
rnb.plot.snp.heatmap    rnb.plot.snp.heatmap
rnb.region.types        rnb.region.types
rnb.region.types.for.analysis
                        rnb.region.types.for.analysis
rnb.remove.annotation   rnb.remove.annotation
rnb.run.analysis        RnBeads Analysis Pipeline
rnb.run.example         rnb.run.example
rnb.run.import          RnBeads Modules in the Analysis Pipeline
rnb.run.xml             rnb.run.xml
rnb.sample.groups       rnb.sample.groups
rnb.sample.replicates   rnb.sample.replicates
rnb.sample.summary.table
                        rnb.sample.summary.table
rnb.save.annotation     rnb.save.annotation
rnb.set.annotation      rnb.set.annotation
rnb.set.annotation.and.cpg.stats
                        rnb.set.annotation.and.cpg.stats
rnb.show.report         rnb.show.report
rnb.step.betadistribution
                        rnb.step.betadistribution
rnb.write.table         rnb.write.table
rnb.xml2options         rnb.xml2options
rowOneSampleTP          rowOneSampleTP
rowPairedTP             rowPairedTP
rowWelchP               rowWelchP
run,RnBClusterRun-method
                        run-methods
run.cross.validation    run.cross.validation
sampleCovgApply,RnBSet-method
                        sampleCovgApply-methods
sampleMethApply,RnBSet-method
                        sampleMethApply-methods
samples,RnBSet-method   samples-methods
save.rnb.diffmeth       save.rnb.diffmeth
save.rnb.set            save.rnb.set
save.tables,RnBDiffMeth-method
                        save.tables-methods
set.covariates.ct       set.covariates.ct
set.covariates.sva      set.covariates.sva
setExecutable,ClusterArchitecture,character,character-method
                        setExecutable-methods
setModuleNumCores,RnBClusterRun,integer,character-method
                        setModuleNumCores-methods
setModuleResourceRequirements,RnBClusterRun,character,character-method
                        setModuleResourceRequirements-methods
sites,RnBSet-method     sites-methods
summarize.regions,RnBSet-method
                        summarize.regions-methods
summarized.regions,RnBSet-method
                        summarized.regions-methods
updateRegionSummaries,RnBSet-method
                        updateRegionSummaries
