Man pages for RnBeads
RnBeads

acceptedRnBeads option values and restrictions
addDiffMethTable-RnBDiffMeth-methodsaddDiffMethTable-methods
addPheno-RnBSet-methodsaddPheno
addRegionSubsegmentsaddRegionSubsegments
annotation-methodsannotation-methods
as.RnBeadRawSetConversion to/from RnBeadRawSet
assembly-methodsassembly-methods
auto.select.rank.cutauto.select.rank.cut
BMIQBMIQ
ClusterArchitecture-classClusterArchitecture Class
ClusterArchitectureSGE-classClusterArchitectureSGE Class
coercion-methodsas("RnBeadSet", "MethyLumiSet")
combine.diffMeth.objscombine.diffMeth.objs
combine-methodscombine-methods
combineTestPvalsMethcombineTestPvalsMeth
computeDiffTab.regioncomputeDiffTab.region
computeDiffTab.sitecomputeDiffTab.site
covg-methodscovg-methods
create.densityScattercreate.densityScatter
create.hex.summary.plotcreate.hex.summary.plot
createReportcreateReport
createReportGgPlotcreateReportGgPlot
createReportPlotcreateReportPlot
create.scatter.dens.pointscreate.scatter.dens.points
data.frame2GRangesdata.frame2GRanges
densRanksdensRanks
destroy-methodsdestroy-methods
destroy-RnBDiffMeth-methodsdestroy-methods
deviation.plot.betadeviation.plot.beta
dim-BigFfMat-methodDimensions of BigFfMat
dpval-methodsdpval-methods
estimateProportionsCPestimateProportionsCP
exportDMRs2regionFileexportDMRs2regionFile
get.adjustment.variablesget.adjustment.variables
get.comparison.grouplabels-RnBDiffMeth-methodsget.comparison.grouplabels-methods
get.comparison.groupsizes-RnBDiffMeth-methodsget.comparison.groupsizes-methods
get.comparison.infoget.comparison.info
get.comparisons-RnBDiffMeth-methodsget.comparisons-methods
get.covariates.ctget.covariates.ct
get.covariates.svaget.covariates.sva
get.covg.thres-RnBDiffMeth-methodsget.covg.thres-methods
get.cpg.statsget.cpg.stats
getExecutable-ClusterArchitecture-methodsgetExecutable-methods
get.filesget.files
getModuleNumCores-RnBClusterRun-methodsgetModuleNumCores-methods
getNumNaMeth-methodsgetNumNaMeth-methods
get.region.types-RnBDiffMeth-methodsget.region.types-methods
get.site.test.method-RnBDiffMeth-methodsget.site.test.method-methods
getSubCmdStr-ClusterArchitecture-methodsgetSubCmdStr-methods
getSubCmdTokens-ClusterArchitecture-methodsgetSubCmdTokens-methods
getSubCmdTokens-ClusterArchitectureSGE-methodsgetSubCmdTokens-methods
get.table-RnBDiffMeth-methodsget.table-methods
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-methods
includes.sites-RnBDiffMeth-methodsincludes.sites-methods
initialize-ClusterArchitecture-methodinitialize.ClusterArchitecture
initialize-ClusterArchitectureSGE-methodinitialize.ClusterArchitectureSGE
initialize-RnBClusterRun-methodinitialize.RnBClusterRun
initialize-RnBDiffMeth-methodinitialize.RnBDiffMeth
intensities.by.colorintensities.by.color
is.valid-RnBDiffMeth-methodsis.valid-methods
join.diffMeth-methodsjoin.diffMeth-methods
limmaPlimmaP
load.region.subsegment.annotationload.region.subsegment.annotation
load.rnb.diffmethload.rnb.diffmeth
load.rnb.setload.rnb.set
logger.argumentlogger.argument
logger.getfileslogger.getfiles
logger.isinitializedlogger.isinitialized
logger.machine.namelogger.machine.name
loggerManagementLog File Management
loggerMessagesWriting text messages to the log file.
logger.validate.filelogger.validate.file
mask.sites.meth-methodsmask.sites.meth-methods
mergeSamples-methodsmergeSamples
meth-methodsmeth-methods
M-methodsM-methods
mval-methodsmval-methods
nsites-methodsnsites-methods
off-methodsoff-methods
parallel.getNumWorkersparallel.getNumWorkers
parallel.isEnabledparallel.isEnabled
parallel.setupparallel.setup
parallel.teardownparallel.teardown
performEnrichment.diffMethperformEnrichment.diffMeth
performGOenrichment.diffMeth.entrezperformGOenrichment.diffMeth.entrez
pheno-methodspheno-methods
qc-methodsqc-methods
read.bed.filesread.bed.files
read.data.dirread.data.dir
read.georead.geo
read.geo.parse.characteristics_ch1read.geo.parse.characteristics_ch1
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-methods
regions-methodsregions-methods
reload-RnBDiffMeth-methodsreload-methods
remove.regions-methodsremove.regions-methods
remove.samples-methodsremove.samples-methods
remove.sites-methodsremove.sites-methods
Report-classReport Class
ReportGgPlot-classReportGgPlot Class
ReportPlot-classReportPlot 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.annotation2data.framernb.annotation2data.frame
rnb.annotation.sizernb.annotation.size
rnb.beta2mvalrnb.beta2mval
rnb.build.indexrnb.build.index
rnb.call.destructorrnb.call.destructor
RnBClusterRun-classRnBClusterRun Class
rnb.color.legendsrnb.color.legends
RnBDiffMeth-classRnBDiffMeth Class
RnBeadClustering-classRnBeadClustering Class
RnBeadRawSet-classRnBeadRawSet-class
RnBeadsAnalysis of genome-scale DNA methylation data with RnBeads
RnBeads.dataRnBeads Annotation Tables
RnBeadSet-classRnBeadSet Class
rnb.execute.age.predictionrnb.execute.age.prediction
rnb.execute.batcheffectsrnb.execute.batcheffects
rnb.execute.batch.qcrnb.execute.batch.qc
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.dreductionrnb.execute.dreduction
rnb.execute.export.csvrnb.execute.export.csv
rnb.execute.filter.summaryrnb.execute.filter.summary
rnb.execute.gender.predictionrnb.execute.gender.prediction
rnb.execute.greedycutrnb.execute.greedycut
rnb.execute.high.coverage.removalrnb.execute.high.coverage.removal
rnb.execute.importrnb.execute.import
rnb.execute.low.coverage.maskingrnb.execute.low.coverage.masking
rnb.execute.na.removalrnb.execute.na.removal
rnb.execute.normalizationrnb.execute.normalization
rnb.execute.qualityrnb.execute.quality
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.age.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
RnBiseqSet-classRnBiseqSet Class
rnb.is.optionrnb.is.option
rnb.load.annotationrnb.load.annotation
rnb.load.sitelistrnb.load.sitelist
rnb.message.plotrnb.message.plot
rnb.mval2betarnb.mval2beta
rnb.optionsRnBeads 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.pheno.categoriesrnb.plot.pheno.categories
rnb.plot.region.profile.densityrnb.plot.region.profiles
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
rnb.region.typesrnb.region.types
rnb.region.types.for.analysisrnb.region.types.for.analysis
rnb.remove.annotationrnb.remove.annotation
rnb.RnBSet.to.bedExport to BED files
rnb.RnBSet.to.bedGraphrnb.RnBSet.to.bedGraph
rnb.RnBSet.to.GRangesListrnb.RnBSet.to.GRangesList
rnb.run.analysisRnBeads Analysis Pipeline
rnb.run.examplernb.run.example
rnb.runsRnBeads Modules in the Analysis Pipeline
rnb.run.xmlrnb.run.xml
rnb.sample.groupsrnb.sample.groups
rnb.sample.replicatesrnb.sample.replicates
rnb.sample.summary.tablernb.sample.summary.table
rnb.save.annotationrnb.save.annotation
rnb.set.annotationrnb.set.annotation
rnb.set.annotation.and.cpg.statsrnb.set.annotation.and.cpg.stats
RnBSet-classRnBSet Class
rnb.show.reportrnb.show.report
rnb.step.betadistributionrnb.step.betadistribution
rnb.write.tablernb.write.table
rnb.xml2optionsrnb.xml2options
rowOneSampleTProwOneSampleTP
rowPairedTProwPairedTP
rowWelchProwWelchP
run.cross.validationrun.cross.validation
run-RnBClusterRun-methodsrun-methods
sampleCovgApply-methodssampleCovgApply-methods
sampleMethApply-methodssampleMethApply-methods
samples-methodssamples-methods
save.rnb.diffmethsave.rnb.diffmeth
save.rnb.setsave.rnb.set
save.tables-RnBDiffMeth-methodssave.tables-methods
set.covariates.ctset.covariates.ct
set.covariates.svaset.covariates.sva
setExecutable-ClusterArchitecture-methodssetExecutable-methods
setModuleNumCores-RnBClusterRun-methodssetModuleNumCores-methods
setModuleResourceRequirements-RnBClusterRun-methodssetModuleResourceRequirements-methods
sites-methodssites-methods
sub-BigFfMat-ANY-ANY-ANY-methodExtract parts of BigFfMat
subset-BigFfMat-ANY-ANY-ANY-methodReplace parts of BigFfMat
summarized.regions-methodssummarized.regions-methods
summarize.regions-methodssummarize.regions-methods
U-methodsU-methods
updateRegionSummariesupdateRegionSummaries
RnBeads documentation built on May 31, 2017, 11:35 a.m.