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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

License

GPL-3

Maintainer

Fabian Mueller

Last Published

February 15th, 2017

Functions in RnBeads (1.4.0)

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