RnBeads-package	RnBeads
accepted	accepted
addDiffMethTable	addDiffMethTable-RnBDiffMeth-methods
addDiffMethTable,RnBDiffMeth-method	addDiffMethTable-RnBDiffMeth-methods
addPheno	addPheno-RnBSet-methods
addPheno,RnBSet-method	addPheno-RnBSet-methods
addRegionSubsegments	addRegionSubsegments
annotation	annotation-methods
annotation,RnBSet-method	annotation-methods
append.cpg.stats	append.cpg.stats
as.RnBeadRawSet	as.RnBeadRawSet
assembly	assembly-methods
assembly,RnBSet-method	assembly-methods
auto.select.rank.cut	auto.select.rank.cut
BMIQ	BMIQ
ClusterArchitecture-class	ClusterArchitecture-class
ClusterArchitectureSGE-class	ClusterArchitectureSGE-class
coercion-methods	coercion-methods
combine,RnBSet,RnBSet-method	combine-methods
combine,RnBSet-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,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
current	accepted
data.frame2GRanges	data.frame2GRanges
densRanks	densRanks
destroy	destroy-methods
destroy,RnBDiffMeth-method	destroy-RnBDiffMeth-methods
destroy,RnBeadRawSet-method	destroy-methods
destroy,RnBeadSet-method	destroy-methods
destroy,RnBSet-method	destroy-methods
deviation.plot.beta	deviation.plot.beta
dpval	dpval-methods
dpval,RnBeadSet-method	dpval-methods
estimateProportionsCP	estimateProportionsCP
exportDMRs2regionFile	exportDMRs2regionFile
get.adjustment.variables	get.adjustment.variables
get.comparison.grouplabels	get.comparison.grouplabels-RnBDiffMeth-methods
get.comparison.grouplabels,RnBDiffMeth-method	get.comparison.grouplabels-RnBDiffMeth-methods
get.comparison.groupsizes	get.comparison.groupsizes-RnBDiffMeth-methods
get.comparison.groupsizes,RnBDiffMeth-method	get.comparison.groupsizes-RnBDiffMeth-methods
get.comparison.info	get.comparison.info
get.comparisons	get.comparisons-RnBDiffMeth-methods
get.comparisons,RnBDiffMeth-method	get.comparisons-RnBDiffMeth-methods
get.covariates.ct	get.covariates.ct
get.covariates.sva	get.covariates.sva
get.covg.thres	get.covg.thres-RnBDiffMeth-methods
get.covg.thres,RnBDiffMeth-method	get.covg.thres-RnBDiffMeth-methods
get.cpg.stats	get.cpg.stats
get.files	get.files
get.region.types	get.region.types-RnBDiffMeth-methods
get.region.types,RnBDiffMeth-method	get.region.types-RnBDiffMeth-methods
get.site.test.method	get.site.test.method-RnBDiffMeth-methods
get.site.test.method,RnBDiffMeth-method	get.site.test.method-RnBDiffMeth-methods
get.table	get.table-RnBDiffMeth-methods
get.table,RnBDiffMeth-method	get.table-RnBDiffMeth-methods
getExecutable	getExecutable-ClusterArchitecture-methods
getExecutable,ClusterArchitecture,character-method	getExecutable-ClusterArchitecture-methods
getModuleNumCores	getModuleNumCores-RnBClusterRun-methods
getModuleNumCores,RnBClusterRun-method	getModuleNumCores-RnBClusterRun-methods
getSubCmdStr	getSubCmdStr-ClusterArchitecture-methods
getSubCmdStr,ClusterArchitecture-method	getSubCmdStr-ClusterArchitecture-methods
getSubCmdTokens	getSubCmdTokens-ClusterArchitecture-methods
getSubCmdTokens,ClusterArchitecture-method	getSubCmdTokens-ClusterArchitecture-methods
getSubCmdTokens,ClusterArchitectureSGE-method	getSubCmdTokens-ClusterArchitectureSGE-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
hg19	RnBeads.data
infos	accepted
initialize,ClusterArchitecture-method	initialize-ClusterArchitecture-method
initialize,ClusterArchitectureSGE-method	initialize-ClusterArchitectureSGE-method
initialize,Report-method	Report-class
initialize,ReportGgPlot-method	ReportGgPlot-class
initialize,ReportPlot-method	ReportPlot-class
initialize,RnBClusterRun-method	initialize-RnBClusterRun-method
initialize,RnBDiffMeth-method	initialize-RnBDiffMeth-method
initialize,RnBeadClustering-method	RnBeadClustering-class
initialize,RnBeadRawSet-method	RnBeadRawSet-class
initialize,RnBeadSet-method	RnBeadSet-class
initialize,RnBiseqSet-method	RnBiseqSet-class
intensities.by.color	intensities.by.color
is.valid	is.valid-RnBDiffMeth-methods
is.valid,RnBDiffMeth-method	is.valid-RnBDiffMeth-methods
join.diffMeth	join.diffMeth-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.close	loggerManagement
logger.completed	loggerManagement
logger.error	loggerMessages
logger.getfiles	logger.getfiles
logger.info	loggerMessages
logger.isinitialized	logger.isinitialized
logger.machine.name	logger.machine.name
logger.start	loggerManagement
logger.status	loggerMessages
logger.validate.file	logger.validate.file
logger.warning	loggerMessages
M	M-methods
M,RnBeadRawSet-method	M-methods
mergeSamples	mergeSamples-methods
mergeSamples,RnBSet-method	mergeSamples-methods
meth	meth-methods
meth,RnBSet-method	meth-methods
mm10	RnBeads.data
mm9	RnBeads.data
mval	mval-methods
mval,RnBSet-method	mval-methods
off	off-methods
off,Report-method	off-methods
off,ReportGgPlot-method	off-methods
off,ReportPlot-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	pheno-methods
pheno,RnBSet-method	pheno-methods
previous	accepted
qc	qc-methods
qc,RnBeadSet-method	qc-methods
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.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,RnBSet-method	regionMapping-methods
regions	regions-methods
regions,RnBSet-method	regions-methods
reload	reload-RnBDiffMeth-methods
reload,RnBDiffMeth-method	reload-RnBDiffMeth-methods
remove.samples	remove.samples-methods
remove.samples,RnBeadRawSet-method	remove.samples-methods
remove.samples,RnBeadSet-method	remove.samples-methods
remove.samples,RnBSet-method	remove.samples-methods
remove.sites	remove.sites-methods
remove.sites,RnBeadRawSet-method	remove.sites-methods
remove.sites,RnBeadSet-method	remove.sites-methods
remove.sites,RnBSet-method	remove.sites-methods
Report-class	Report-class
ReportGgPlot-class	ReportGgPlot-class
ReportPlot-class	ReportPlot-class
rn5	RnBeads.data
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.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.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.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	rnb.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.sitelist	rnb.load.sitelist
rnb.message.plot	rnb.message.plot
rnb.mval2beta	rnb.mval2beta
rnb.options	rnb.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.profile.density
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.RnBSet.to.bed	rnb.RnBSet.to.bed
rnb.RnBSet.to.bedGraph	rnb.RnBSet.to.bedGraph
rnb.RnBSet.to.GRangesList	rnb.RnBSet.to.GRangesList
rnb.run.analysis	rnb.run.analysis
rnb.run.differential	rnb.runs
rnb.run.example	rnb.run.example
rnb.run.exploratory	rnb.runs
rnb.run.import	rnb.runs
rnb.run.inference	rnb.runs
rnb.run.preprocessing	rnb.runs
rnb.run.qc	rnb.runs
rnb.run.tnt	rnb.runs
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,RnBSet-method	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
RnBClusterRun-class	RnBClusterRun-class
RnBDiffMeth-class	RnBDiffMeth-class
RnBeadClustering-class	RnBeadClustering-class
RnBeadRawSet	RnBeadRawSet-class
RnBeadRawSet-class	RnBeadRawSet-class
RnBeads	RnBeads
RnBeads.data	RnBeads.data
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-RnBClusterRun-methods
run,RnBClusterRun-method	run-RnBClusterRun-methods
samples	samples-methods
samples,RnBeadClustering-method	samples-methods
samples,RnBSet-method	samples-methods
save.rnb.diffmeth	save.rnb.diffmeth
save.rnb.set	save.rnb.set
save.tables	save.tables-RnBDiffMeth-methods
save.tables,RnBDiffMeth-method	save.tables-RnBDiffMeth-methods
set.covariates.ct	set.covariates.ct
set.covariates.sva	set.covariates.sva
setExecutable	setExecutable-ClusterArchitecture-methods
setExecutable,ClusterArchitecture,character,character-method	setExecutable-ClusterArchitecture-methods
setModuleNumCores	setModuleNumCores-RnBClusterRun-methods
setModuleNumCores,RnBClusterRun,integer,character-method	setModuleNumCores-RnBClusterRun-methods
setModuleResourceRequirements	setModuleResourceRequirements-RnBClusterRun-methods
setModuleResourceRequirements,RnBClusterRun,character,character-method	setModuleResourceRequirements-RnBClusterRun-methods
sites	sites-methods
sites,RnBSet-method	sites-methods
summarize.regions	summarize.regions-methods
summarize.regions,RnBSet-method	summarize.regions-methods
summarized.regions	summarized.regions-methods
summarized.regions,RnBSet-method	summarized.regions-methods
U	U-methods
U,RnBeadRawSet-method	U-methods
updateRegionSummaries	updateRegionSummaries
updateRegionSummaries,RnBSet-method	updateRegionSummaries
