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RnBeads (version 1.4.0)
RnBeads
Description
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
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Version
Version
1.4.0
1.2.0
1.0.0
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Version
1.4.0
License
GPL-3
Maintainer
Fabian Mueller
Last Published
March 20th, 2016
Functions in RnBeads (1.4.0)
Search functions
M,RnBeadRawSet-method
M-methods
RnBiseqSet-class
RnBiseqSet Class
create.densityScatter
create.densityScatter
get.adjustment.variables
get.adjustment.variables
destroy,RnBDiffMeth-method
destroy-methods
accepted
RnBeads option values and restrictions
computeDiffTab.default.region
computeDiffTab.region
ReportGgPlot-class
ReportGgPlot Class
get.files
get.files
addDiffMethTable,RnBDiffMeth-method
addDiffMethTable-methods
get.site.test.method,RnBDiffMeth-method
get.site.test.method-methods
BMIQ
BMIQ
auto.select.rank.cut
auto.select.rank.cut
computeDiffTab.default.site
computeDiffTab.site
destroy,RnBSet-method
destroy-methods
getExecutable,ClusterArchitecture,character-method
getExecutable-methods
RnBDiffMeth-class
RnBDiffMeth Class
create.hex.summary.plot
create.hex.summary.plot
covg,RnBSet-method
covg-methods
RnBeadClustering-class
RnBeadClustering Class
RnBeads
Analysis of genome-scale DNA methylation data with RnBeads
has.covariates.ct
has.covariates.ct
load.rnb.diffmeth
load.rnb.diffmeth
intensities.by.color
intensities.by.color
get.comparison.info
get.comparison.info
ClusterArchitecture-class
ClusterArchitecture Class
includes.sites,RnBDiffMeth-method
includes.sites-methods
logger.getfiles
logger.getfiles
greedycut.get.statistics
greedycut.get.statistics
densRanks
densRanks
logger.isinitialized
logger.isinitialized
pheno,RnBSet-method
pheno-methods
performEnrichment.diffMeth
performEnrichment.diffMeth
get.region.types,RnBDiffMeth-method
get.region.types-methods
off,Report-method
off-methods
read.bed.files
read.bed.files
logger.argument
logger.argument
mval,RnBSet-method
mval-methods
rnb.execute.dreduction
rnb.execute.dreduction
dpval,RnBeadSet-method
dpval-methods
parallel.getNumWorkers
parallel.getNumWorkers
regions,RnBSet-method
regions-methods
rnb.add.section
rnb.add.section
read.geo.parse.characteristics_ch1
read.geo.parse.characteristics_ch1
exportDMRs2regionFile
exportDMRs2regionFile
get.covariates.ct
get.covariates.ct
rnb.export.annotation
rnb.export.annotation
is.valid,RnBDiffMeth-method
is.valid-methods
remove.sites,RnBSet-method
remove.sites-methods
rnb.execute.computeDiffMeth
rnb.execute.computeDiffMeth
remove.samples,RnBSet-method
remove.samples-methods
rnb.execute.import
rnb.execute.import
rnb.execute.clustering
rnb.execute.clustering
rnb.build.index
rnb.build.index
rnb.execute.snp.removal
rnb.execute.snp.removal
rnb.add.figure
rnb.add.figure
rnb.execute.sva
rnb.execute.sva
rnb.plot.dreduction
rnb.plot.dreduction
rnb.annotation2data.frame
rnb.annotation2data.frame
rnb.execute.clustering.all
rnb.execute.clustering.all
rnb.add.reference
rnb.add.reference
rnb.plot.num.sites.covg
rnb.plot.num.sites.covg
RnBClusterRun-class
RnBClusterRun Class
rnb.execute.sex.removal
rnb.execute.sex.removal
Report-class
Report Class
load.rnb.set
load.rnb.set
rnb.plot.marker.fstat
rnb.plot.marker.fstat
rnb.plot.ct.heatmap
rnb.plot.ct.heatmap
as.RnBeadRawSet
as("MethyLumiSet", "RnBeadRawSet")
rnb.run.xml
rnb.run.xml
rnb.plot.control.boxplot
rnb.plot.control.boxplot
rnb.xml2options
rnb.xml2options
rnb.get.reliability.matrix
rnb.get.reliability.matrix
rnb.plot.region.profile.density
rnb.plot.region.profiles
rnb.find.relative.site.coord
rnb.find.relative.site.coord
rnb.is.option
rnb.is.option
setExecutable,ClusterArchitecture,character,character-method
setExecutable-methods
sampleMethApply,RnBSet-method
sampleMethApply-methods
rnb.plot.sentrix.distribution
rnb.plot.sentrix.distribution
createReport
createReport
save.rnb.set
save.rnb.set
rnb.infinium.control.targets
rnb.infinium.control.targets
logger.start
Log File Management
rnb.message.plot
rnb.message.plot
rnb.plot.beta.comparison
rnb.plot.beta.comparison
rnb.plot.region.profiles
rnb.plot.region.profiles
rowWelchP
rowWelchP
rnb.run.example
rnb.run.example
rnb.plot.biseq.coverage
rnb.plot.biseq.coverage
get.comparison.grouplabels,RnBDiffMeth-method
get.comparison.grouplabels-methods
rnb.set.annotation.and.cpg.stats
rnb.set.annotation.and.cpg.stats
parallel.teardown
parallel.teardown
get.covariates.sva
get.covariates.sva
get.covg.thres,RnBDiffMeth-method
get.covg.thres-methods
rnb.run.import
RnBeads Modules in the Analysis Pipeline
rnb.set.annotation
rnb.set.annotation
rnb.execute.batcheffects
rnb.execute.batcheffects
setModuleNumCores,RnBClusterRun,integer,character-method
setModuleNumCores-methods
rnb.plot.betadistribution.probeCategories
rnb.plot.betadistribution.probeCategories
rnb.execute.high.coverage.removal
rnb.execute.high.coverage.removal
rnb.write.table
rnb.write.table
get.table,RnBDiffMeth-method
get.table-methods
getSubCmdTokens,ClusterArchitectureSGE-method
getSubCmdTokens-methods
rnb.execute.context.removal
rnb.execute.context.removal
initialize,ClusterArchitectureSGE-method
initialize.ClusterArchitectureSGE
hasCovg,RnBSet-method
hasCovg-methods
rnb.execute.export.csv
rnb.execute.export.csv
greedycut.filter.matrix
greedycut.filter.matrix
rnb.plot.biseq.coverage.hist
rnb.plot.biseq.coverage.hist
rnb.region.types.for.analysis
rnb.region.types.for.analysis
logger.status
Writing text messages to the log file.
logger.validate.file
logger.validate.file
rnb.add.tables
rnb.add.tables
rnb.execute.gender.prediction
rnb.execute.gender.prediction
rnb.plot.locus.profile
rnb.plot.locus.profile
ReportPlot-class
ReportPlot Class
rnb.plot.snp.heatmap
rnb.plot.snp.heatmap
rnb.get.reference
rnb.get.reference
set.covariates.ct
set.covariates.ct
rnb.sample.replicates
rnb.sample.replicates
RnBeadRawSet-class
RnBeadRawSet-class
rnb.get.mapping
rnb.get.mapping
rnb.plot.control.barplot
rnb.plot.control.barplot
combine,RnBSet,RnBSet-method
combine-methods
assembly,RnBSet-method
assembly-methods
createReportGgPlot
createReportGgPlot
rnb.plot.snp.boxplot
rnb.plot.snp.boxplot
updateRegionSummaries,RnBSet-method
updateRegionSummaries
deviation.plot.beta
deviation.plot.beta
samples,RnBSet-method
samples-methods
RnBeadSet-class
RnBeadSet Class
combine.diffMeth.objs
combine.diffMeth.objs
get.comparisons,RnBDiffMeth-method
get.comparisons-methods
join.diffMeth,RnBDiffMeth,RnBDiffMeth-method
join.diffMeth-methods
combineTestPvalsMeth
combineTestPvalsMeth
annotation,RnBSet-method
annotation-methods
data.frame2GRanges
data.frame2GRanges
parallel.isEnabled
parallel.isEnabled
performGOenrichment.diffMeth.entrez
performGOenrichment.diffMeth.entrez
qc,RnBeadSet-method
qc-methods
estimateProportionsCP
estimatePropotionsCP
read.single.bed
read.single.bed
getModuleNumCores,RnBClusterRun-method
getModuleNumCores-methods
read.sample.annotation
read.sample.annotation
getSubCmdTokens,ClusterArchitecture-method
getSubCmdTokens-methods
greedycut.get.submatrix
greedycut.get.submatrix
limmaP
limmaP
read.GS.report
read.GS.report
rnb.RnBSet.to.GRangesList
rnb.RnBSet.to.GRangesList
rnb.add.list
rnb.add.list
rnb.execute.cross.reactive.removal
rnb.execute.cross.reactive.removal
mergeSamples,RnBSet-method
mergeSamples
read.data.dir
read.data.dir
get.comparison.groupsizes,RnBDiffMeth-method
get.comparison.groupsizes-methods
rnb.RnBSet.to.bed
rnb.RnBSet.to.bed
refFreeEWASP
refFreeEWASP
rnb.add.paragraph
rnb.add.paragraph
rnb.beta2mval
rnb.beta2mval
initialize,RnBClusterRun-method
initialize.RnBClusterRun
rnb.export.to.ewasher
rnb.export.to.ewasher
rnb.color.legends
rnb.color.legends
rnb.execute.batch.qc
rnb.execute.batch.qc
rnb.performance.profile
rnb.performance.profile
rnb.execute.low.coverage.masking
rnb.execute.low.coverage.masking
rnb.plot.sentrix.distributions
rnb.plot.sentrix.distributions
rnb.plot.coverage.thresholds
rnb.plot.coverage.thresholds
rnb.call.destructor
rnb.call.destructor
rnb.execute.filter.summary
rnb.execute.filter.summary
rnb.execute.quality
rnb.execute.quality
rnb.plot.snp.barplot
rnb.plot.snp.barplot
rnb.execute.na.removal
rnb.execute.na.removal
rnb.execute.normalization
rnb.execute.normalization
rnb.get.directory
rnb.get.directory
rnb.sample.groups
rnb.sample.groups
sampleCovgApply,RnBSet-method
sampleCovgApply-methods
summarize.regions,RnBSet-method
summarize.regions-methods
rnb.show.report
rnb.show.report
rnb.run.analysis
RnBeads Analysis Pipeline
run,RnBClusterRun-method
run-methods
rnb.initialize.reports
rnb.initialize.reports
rnb.load.annotation
rnb.load.annotation
rnb.mval2beta
rnb.mval2beta
rnb.plot.betadistribution.sampleGroups
rnb.plot.betadistribution.sampleGroups
setModuleResourceRequirements,RnBClusterRun,character,character-method
setModuleResourceRequirements-methods
rnb.remove.annotation
rnb.remove.annotation
rnb.sample.summary.table
rnb.sample.summary.table
rnb.save.annotation
rnb.save.annotation
rowOneSampleTP
rowOneSampleTP
ClusterArchitectureSGE-class
ClusterArchitectureSGE Class
addRegionSubsegments
addRegionSubsegments
addPheno,RnBSet-method
addPheno
coercion-methods
as("RnBeadSet", "MethyLumiSet")
create.scatter.dens.points
create.scatter.dens.points
has.covariates.sva
has.covariates.sva
load.region.subsegment.annotation
load.region.subsegment.annotation
remove.regions,RnBSet-method
remove.regions-methods
rnb.execute.greedycut
rnb.execute.greedycut
rnb.get.assemblies
rnb.get.assemblies
rnb.options
RnBeads Options
rnb.get.annotation
rnb.get.annotation
rnb.step.betadistribution
rnb.step.betadistribution
rnb.plot.region.site.density
rnb.plot.region.site.density
rnb.region.types
rnb.region.types
save.tables,RnBDiffMeth-method
save.tables-methods
set.covariates.sva
set.covariates.sva
get.cpg.stats
get.cpg.stats
getSubCmdStr,ClusterArchitecture-method
getSubCmdStr-methods
initialize,RnBDiffMeth-method
initialize.RnBDiffMeth
logger.machine.name
logger.machine.name
meth,RnBSet-method
meth-methods
parallel.setup
parallel.setup
read.idat.files2
read.idat.files2
reload,RnBDiffMeth-method
reload-methods
rnb.execute.ct.estimation
rnb.execute.ct.estimation
rnb.export.to.trackhub
rnb.export.to.trackhub
rnb.get.chromosomes
rnb.get.chromosomes
rnb.options2xml
rnb.options2xml
rnb.plot.biseq.coverage.violin
rnb.plot.biseq.coverage.violin
rnb.plot.negative.boxplot
rnb.plot.negative.boxplot
save.rnb.diffmeth
save.rnb.diffmeth
RnBeads.data
RnBeads Annotation Tables
U,RnBeadRawSet-method
U-methods
RnBSet-class
RnBSet Class
createReportPlot
createReportPlot
initialize,ClusterArchitecture-method
initialize.ClusterArchitecture
nsites,RnBSet-method
nsites-methods
read.geo
read.geo
read.idat.files
read.idat.files
regionMapping,RnBSet-method
regionMapping-methods
rnb.RnBSet.to.bedGraph
rnb.RnBSet.to.bedGraph
rnb.add.table
rnb.add.table
rnb.annotation.size
rnb.annotation.size
rnb.execute.tnt
rnb.execute.tnt
rnb.execute.variability.removal
rnb.execute.variability.removal
rnb.export.all.annotation
rnb.export.all.annotation
rnb.load.sitelist
rnb.load.sitelist
rnb.plot.pheno.categories
rnb.plot.pheno.categories
rowPairedTP
rowPairedTP
summarized.regions,RnBSet-method
summarized.regions-methods
sites,RnBSet-method
sites-methods