# RnBeads

## Documentation for package ‘RnBeads’ version 2.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E G H I J L M N O P Q R S U misc

RnBeads-package | Analysis of genome-scale DNA methylation data with RnBeads

## -- A --

accepted | RnBeads option values and restrictions
addDiffMethTable | addDiffMethTable-methods
addDiffMethTable-method | addDiffMethTable-methods
addPheno | addPheno
addPheno-method | addPheno
addRegionSubsegments | addRegionSubsegments
annotation | annotation-methods
annotation-method | annotation-methods
apply.iEVORA | apply.iEVORA
as.RnBeadRawSet | Conversion to/from RnBeadRawSet
assembly | assembly-methods
assembly-method | assembly-methods
auto.select.rank.cut | auto.select.rank.cut

## -- B --

BMIQ | BMIQ

## -- C --

ClusterArchitecture-class | ClusterArchitecture Class
ClusterArchitectureSGE-class | ClusterArchitectureSGE Class
coercion-methods | as("RnBeadSet", "MethyLumiSet")
cols.to.rank.region | cols.to.rank.site
cols.to.rank.site | cols.to.rank.site
combine | combine-methods
combine-method | combine-methods
combine.diffMeth.objs | combine.diffMeth.objs
combineTestPvalsMeth | combineTestPvalsMeth
computeDiffTab.default.region | computeDiffTab.region
computeDiffTab.default.site | computeDiffTab.site
computeDiffTab.extended.site | computeDiffTab.site
computeDiffTab.region | computeDiffTab.region
computeDiffTab.site | computeDiffTab.site
covg | covg-methods
covg-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
current | RnBeads option values and restrictions

## -- D --

data.frame2GRanges | data.frame2GRanges
densRanks | densRanks
destroy | destroy-methods
destroy-method | destroy-methods
destroy-method | destroy-methods
deviation.plot.beta | deviation.plot.beta
diffVar | diffVar
dim-method | Dimensions of BigFfMat
downloadLolaDbs | downloadLolaDbs
dpval | dpval-methods
dpval-method | dpval-methods

## -- E --

estimateProportionsCP | estimateProportionsCP
exportDMRs2regionFile | exportDMRs2regionFile

## -- G --

get.adjustment.variables | get.adjustment.variables
get.comparison.grouplabels | get.comparison.grouplabels-methods
get.comparison.grouplabels-method | get.comparison.grouplabels-methods
get.comparison.groupsizes | get.comparison.groupsizes-methods
get.comparison.groupsizes-method | get.comparison.groupsizes-methods
get.comparison.info | get.comparison.info
get.comparisons | get.comparisons-methods
get.comparisons-method | get.comparisons-methods
get.covariates.ct | get.covariates.ct
get.covariates.sva | get.covariates.sva
get.covg.thres | get.covg.thres-methods
get.covg.thres-method | get.covg.thres-methods
get.cpg.stats | get.cpg.stats
get.files | get.files
get.region.types | get.region.types-methods
get.region.types-method | get.region.types-methods
get.site.test.method | get.site.test.method-methods
get.site.test.method-method | get.site.test.method-methods
get.table | get.table-methods
get.table-method | get.table-methods
get.table.ids | Returns the colum names of the differential variability table.
get.variability.method | get.variability.method-methods
get.variability.method-method | get.variability.method-methods
getCellTypesFromLolaDb | getCellTypesFromLolaDb
getExecutable | getExecutable-methods
getExecutable-method | getExecutable-methods
getModuleNumCores | getModuleNumCores-methods
getModuleNumCores-method | getModuleNumCores-methods
getNamesFromLolaDb | getNamesFromLolaDb
getNumNaMeth | getNumNaMeth-methods
getNumNaMeth-method | getNumNaMeth-methods
getSubCmdStr | getSubCmdStr-methods
getSubCmdStr-method | getSubCmdStr-methods
getSubCmdTokens | getSubCmdTokens-methods
getSubCmdTokens-method | getSubCmdTokens-methods
getSubCmdTokens-method | getSubCmdTokens-methods
getTargetFromLolaDb | getTargetFromLolaDb
greedycut.filter.matrix | greedycut.filter.matrix
greedycut.get.statistics | greedycut.get.statistics
greedycut.get.submatrix | greedycut.get.submatrix

## -- H --

has.covariates.ct | has.covariates.ct
has.covariates.sva | has.covariates.sva
hasCovg | hasCovg-methods
hasCovg-method | hasCovg-methods

## -- I --

includes.sites | includes.sites-methods
includes.sites-method | includes.sites-methods
infos | RnBeads option values and restrictions
initialize-method | Report Class
initialize-method | ReportGgPlot Class
initialize-method | ReportPlot Class
initialize-method | RnBeadClustering Class
initialize-method | RnBeadRawSet-class
initialize-method | RnBeadSet Class
initialize-method | RnBiseqSet Class
initialize-method | initialize.ClusterArchitecture
initialize-method | initialize.ClusterArchitectureSGE
initialize-method | initialize.RnBClusterRun
initialize-method | initialize.RnBDiffMeth
intensities.by.color | intensities.by.color
is.valid | is.valid-methods
is.valid-method | is.valid-methods
isImputed | isImputed
isImputed-method | isImputed

## -- J --

join.diffMeth | join.diffMeth-methods
join.diffMeth-method | join.diffMeth-methods

## -- L --

limmaP | limmaP
load.region.subsegment.annotation | load.region.subsegment.annotation
load.rnb.diffmeth | load.rnb.diffmeth
load.rnb.set | load.rnb.set
loadLolaDbs | loadLolaDbs
logger.argument | logger.argument
logger.close | Log File Management
logger.completed | Log File Management
logger.error | Writing text messages to the log file.
logger.getfiles | logger.getfiles
logger.info | Writing text messages to the log file.
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
logger.warning | Writing text messages to the log file.
lolaBarPlot | lolaBarPlot
lolaBoxPlotPerTarget | lolaBoxPlotPerTarget
lolaVolcanoPlot | lolaVolcanoPlot
lump.hg19 | LUMP Support
lump.hg38 | LUMP Support (hg38)

## -- M --

M | M-methods
M-method | M-methods
mask.sites.meth | mask.sites.meth-methods
mask.sites.meth-method | mask.sites.meth-methods
mergeSamples | mergeSamples
mergeSamples-method | mergeSamples
meth | meth-methods
meth-method | meth-methods
mval | mval-methods
mval-method | mval-methods

## -- N --

nsites | nsites-methods
nsites-method | nsites-methods

## -- O --

off | off-methods
off-method | off-methods

## -- P --

parallel.getNumWorkers | parallel.getNumWorkers
parallel.isEnabled | parallel.isEnabled
parallel.setup | parallel.setup
parallel.teardown | parallel.teardown
performGoEnrichment.diffMeth | performGoEnrichment.diffMeth
performGOenrichment.diffMeth.entrez | performGOenrichment.diffMeth.entrez
performGOEnrichment.diffVar | performGOEnrichment.diffVar
performLolaEnrichment.diffMeth | performLolaEnrichment.diffMeth
performLolaEnrichment.diffVar | performLolaEnrichment.diffVar
pheno | pheno-methods
pheno-method | pheno-methods
prepareSOFTfileForGEO | prepareSOFTfileForGEO
previous | RnBeads option values and restrictions

## -- Q --

qc | qc-methods
qc-method | qc-methods

## -- R --

read.bed.files | read.bed.files
read.data.dir | read.data.dir
read.GS.report | read.GS.report
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 | regionMapping-methods
regionMapping-method | regionMapping-methods
regions | regions-methods
regions-method | regions-methods
reload | reload-methods
reload-method | reload-methods
remove.regions | remove.regions-methods
remove.regions-method | remove.regions-methods
remove.samples | remove.samples-methods
remove.samples-method | remove.samples-methods
remove.sites | remove.sites-methods
remove.sites-method | remove.sites-methods
Report-class | Report Class
ReportGgPlot-class | ReportGgPlot Class
ReportPlot-class | ReportPlot Class
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.combine.arrays | Combine array-based datasets
rnb.combine.seq | rnb.combine.seq
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.diffVar | rnb.execute.diffVar
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.genomewide | Genome-wide methylation level
rnb.execute.greedycut | rnb.execute.greedycut
rnb.execute.high.coverage.removal | rnb.execute.high.coverage.removal
rnb.execute.import | rnb.execute.import
rnb.execute.imputation | rnb.execute.imputation
rnb.execute.low.coverage.masking | rnb.execute.low.coverage.masking
rnb.execute.lump | Leukocytes unmethylation for purity
rnb.execute.na.removal | rnb.execute.na.removal
rnb.execute.normalization | rnb.execute.normalization
rnb.execute.quality | rnb.execute.quality
rnb.execute.sex.prediction | rnb.execute.sex.prediction
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.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.getOption | RnBeads Options
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.annotation.from.db | rnb.load.annotation.from.db
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.read.geo | Import methylation data from GEO
rnb.region.types | rnb.region.types
rnb.region.types.for.analysis | rnb.region.types.for.analysis
rnb.remove.annotation | rnb.remove.annotation
rnb.RnBSet.to.bed | Export to BED files
rnb.RnBSet.to.bedGraph | rnb.RnBSet.to.bedGraph
rnb.RnBSet.to.GRangesList | rnb.RnBSet.to.GRangesList
rnb.run.analysis | RnBeads Analysis Pipeline
rnb.run.differential | RnBeads Modules in the Analysis Pipeline
rnb.run.dj | rnb.run.dj
rnb.run.example | rnb.run.example
rnb.run.exploratory | RnBeads Modules in the Analysis Pipeline
rnb.run.import | RnBeads Modules in the Analysis Pipeline
rnb.run.inference | RnBeads Modules in the Analysis Pipeline
rnb.run.preprocessing | RnBeads Modules in the Analysis Pipeline
rnb.run.qc | RnBeads Modules in the Analysis Pipeline
rnb.run.tnt | 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.sample.summary.table-method | rnb.sample.summary.table
rnb.save.annotation | rnb.save.annotation
rnb.section.diffVar.region | rnb.section.diffVar.region
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.step.cnv | rnb.step.cnv
rnb.write.table | rnb.write.table
rnb.xml2options | rnb.xml2options
RnBClusterRun-class | RnBClusterRun Class
RnBDiffMeth-class | RnBDiffMeth Class
RnBeadClustering-class | RnBeadClustering Class
RnBeadRawSet | RnBeadRawSet-class
RnBeadRawSet-class | RnBeadRawSet-class
RnBeads | Analysis of genome-scale DNA methylation data with RnBeads
RnBeads.data | RnBeads Annotation Tables
RnBeadSet | RnBeadSet Class
RnBeadSet-class | RnBeadSet Class
RnBiseqSet | RnBiseqSet Class
RnBiseqSet-class | RnBiseqSet Class
RnBSet-class | RnBSet Class
rowOneSampleTP | rowOneSampleTP
rowPairedTP | rowPairedTP
rowWelchP | rowWelchP
run | run-methods
run-method | run-methods
run.cross.validation | run.cross.validation

## -- S --

sampleCovgApply | sampleCovgApply-methods
sampleCovgApply-method | sampleCovgApply-methods
sampleMethApply | sampleMethApply-methods
sampleMethApply-method | sampleMethApply-methods
samples | samples-methods
samples-method | samples-methods
save.rnb.diffmeth | save.rnb.diffmeth
save.rnb.set | save.rnb.set
save.tables | save.tables-methods
save.tables-method | save.tables-methods
set.covariates.ct | set.covariates.ct
set.covariates.sva | set.covariates.sva
setExecutable | setExecutable-methods
setExecutable-method | setExecutable-methods
setModuleNumCores | setModuleNumCores-methods
setModuleNumCores-method | setModuleNumCores-methods
setModuleResourceRequirements | setModuleResourceRequirements-methods
setModuleResourceRequirements-method | setModuleResourceRequirements-methods
sites | sites-methods
sites-method | sites-methods
summarize.regions | summarize.regions-methods
summarize.regions-method | summarize.regions-methods
summarized.regions | summarized.regions-methods
summarized.regions-method | summarized.regions-methods

## -- U --

U | U-methods
U-method | U-methods
updateMethylationSites | updateMethylationSites-methods
updateMethylationSites-method | updateMethylationSites-methods
updateRegionSummaries | updateRegionSummaries
updateRegionSummaries-method | updateRegionSummaries

## -- misc --

[-method | Extract parts of BigFfMat
[<--method | Replace parts of BigFfMat