RnBeads: RnBeads

RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.

AuthorYassen Assenov [aut], Pavlo Lutsik [aut], Fabian Mueller [aut, cre]
Date of publicationNone
MaintainerFabian Mueller <rnbeads@mpi-inf.mpg.de>
LicenseGPL-3
Version1.6.1

View on Bioconductor

Man pages

accepted: RnBeads option values and restrictions

add.agecomparison.plot: add.agecomparison.plot

add.age.histogram: add.age.histogram

add.combination.plot: add.combination.plot

addDiffMethTable-RnBDiffMeth-methods: addDiffMethTable-methods

add.error.plot: add.error.plot

addPheno-RnBSet-methods: addPheno

add.quantile.plot: add.quantile.plot

addRegionSubsegments: addRegionSubsegments

age.anti.transformation: age.anti.transformation

agePredictor: agePredictor

agePredictor450: agePredictor450

agePredictorRRBS: agePredictorRRBS

age.transformation: age.transformation

annotation-methods: annotation-methods

as.RnBeadRawSet: as("MethyLumiSet", "RnBeadRawSet")

assembly-methods: assembly-methods

auto.select.rank.cut: auto.select.rank.cut

BMIQ: BMIQ

ClusterArchitecture-class: ClusterArchitecture Class

ClusterArchitectureSGE-class: ClusterArchitectureSGE Class

coercion-methods: as("RnBeadSet", "MethyLumiSet")

combine.diffMeth.objs: combine.diffMeth.objs

combine-methods: combine-methods

combineTestPvalsMeth: combineTestPvalsMeth

computeDiffTab.region: computeDiffTab.region

computeDiffTab.site: computeDiffTab.site

covg-methods: covg-methods

create.densityScatter: create.densityScatter

create.hex.summary.plot: create.hex.summary.plot

createPredictor: createPredictor

createReport: createReport

createReportGgPlot: createReportGgPlot

createReportPlot: createReportPlot

create.scatter.dens.points: create.scatter.dens.points

cv.array: cv.array

cv.biseq: cv.biseq

data.frame2GRanges: data.frame2GRanges

densRanks: densRanks

destroy-methods: destroy-methods

destroy-RnBDiffMeth-methods: destroy-methods

deviation.plot.beta: deviation.plot.beta

dpval-methods: dpval-methods

estimateProportionsCP: estimateProportionsCP

exportDMRs2regionFile: exportDMRs2regionFile

general.cv: general.cv

get.adjustment.variables: get.adjustment.variables

get.comparison.grouplabels-RnBDiffMeth-methods: get.comparison.grouplabels-methods

get.comparison.groupsizes-RnBDiffMeth-methods: get.comparison.groupsizes-methods

get.comparison.info: get.comparison.info

get.comparisons-RnBDiffMeth-methods: get.comparisons-methods

get.covariates.ct: get.covariates.ct

get.covariates.sva: get.covariates.sva

get.covg.thres-RnBDiffMeth-methods: get.covg.thres-methods

get.cpg.stats: get.cpg.stats

getExecutable-ClusterArchitecture-methods: getExecutable-methods

get.files: get.files

getModuleNumCores-RnBClusterRun-methods: getModuleNumCores-methods

get.region.types-RnBDiffMeth-methods: get.region.types-methods

get.site.test.method-RnBDiffMeth-methods: get.site.test.method-methods

getSubCmdStr-ClusterArchitecture-methods: getSubCmdStr-methods

getSubCmdTokens-ClusterArchitecture-methods: getSubCmdTokens-methods

getSubCmdTokens-ClusterArchitectureSGE-methods: getSubCmdTokens-methods

get.table-RnBDiffMeth-methods: get.table-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

hasCovg-methods: hasCovg-methods

imputeRRBS: imputeRRBS

includes.sites-RnBDiffMeth-methods: includes.sites-methods

initialize-ClusterArchitecture-method: initialize.ClusterArchitecture

initialize-ClusterArchitectureSGE-method: initialize.ClusterArchitectureSGE

initialize-RnBClusterRun-method: initialize.RnBClusterRun

initialize-RnBDiffMeth-method: initialize.RnBDiffMeth

intensities.by.color: intensities.by.color

is.valid-RnBDiffMeth-methods: is.valid-methods

join.diffMeth-methods: 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.getfiles: logger.getfiles

logger.isinitialized: logger.isinitialized

logger.machine.name: logger.machine.name

loggerManagement: Log File Management

loggerMessages: Writing text messages to the log file.

logger.validate.file: logger.validate.file

mergeSamples-methods: mergeSamples

meth-methods: meth-methods

M-methods: M-methods

mval-methods: mval-methods

nsites-methods: nsites-methods

off-methods: 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-methods: pheno-methods

qc-methods: 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-methods: regionMapping-methods

regions-methods: regions-methods

reload-RnBDiffMeth-methods: reload-methods

remove.regions-methods: remove.regions-methods

remove.samples-methods: remove.samples-methods

remove.sites-methods: 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.annotation2data.frame: rnb.annotation2data.frame

rnb.annotation.size: rnb.annotation.size

rnb.beta2mval: rnb.beta2mval

rnb.build.index: rnb.build.index

rnb.call.destructor: rnb.call.destructor

RnBClusterRun-class: RnBClusterRun Class

rnb.color.legends: rnb.color.legends

RnBDiffMeth-class: RnBDiffMeth Class

RnBeadClustering-class: RnBeadClustering Class

RnBeadRawSet-class: RnBeadRawSet-class

RnBeads: Analysis of genome-scale DNA methylation data with RnBeads

RnBeads.data: RnBeads Annotation Tables

RnBeadSet-class: RnBeadSet Class

rnb.execute.age.prediction: rnb.execute.age.prediction

rnb.execute.batcheffects: rnb.execute.batcheffects

rnb.execute.batch.qc: rnb.execute.batch.qc

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.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.training: rnb.execute.age.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.infinium.control.targets: rnb.infinium.control.targets

rnb.initialize.reports: rnb.initialize.reports

RnBiseqSet-class: RnBiseqSet Class

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: 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.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: RnBeads Analysis Pipeline

rnb.run.example: rnb.run.example

rnb.runs: 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.save.annotation: rnb.save.annotation

rnb.section.ageprediction: rnb.section.ageprediction

rnb.set.annotation: rnb.set.annotation

rnb.set.annotation.and.cpg.stats: rnb.set.annotation.and.cpg.stats

RnBSet-class: RnBSet Class

rnb.show.report: rnb.show.report

rnb.step.ageprediction: rnb.step.ageprediction

rnb.step.betadistribution: rnb.step.betadistribution

rnb.write.table: rnb.write.table

rnb.xml2options: rnb.xml2options

rowOneSampleTP: rowOneSampleTP

rowPairedTP: rowPairedTP

rowWelchP: rowWelchP

run.cross.validation: run.cross.validation

run-RnBClusterRun-methods: run-methods

sampleCovgApply-methods: sampleCovgApply-methods

sampleMethApply-methods: sampleMethApply-methods

samples-methods: samples-methods

save.rnb.diffmeth: save.rnb.diffmeth

save.rnb.set: save.rnb.set

save.tables-RnBDiffMeth-methods: save.tables-methods

set.covariates.ct: set.covariates.ct

set.covariates.sva: set.covariates.sva

setExecutable-ClusterArchitecture-methods: setExecutable-methods

setModuleNumCores-RnBClusterRun-methods: setModuleNumCores-methods

setModuleResourceRequirements-RnBClusterRun-methods: setModuleResourceRequirements-methods

simpleGlmnet: simpleGlmnet

simpleGlmnetEvaluate: simpleGlmnetEvaluate

simpleGlmnetRRBS: simpleGlmnetRRBS

sites-methods: sites-methods

summarized.regions-methods: summarized.regions-methods

summarize.regions-methods: summarize.regions-methods

trainPredictor: trainPredictor

U-methods: U-methods

updateRegionSummaries: updateRegionSummaries

writePredictorToCsv: writePredictorToCsv

Functions

accepted Man page
add.agecomparison.plot Man page
add.age.histogram Man page
add.combination.plot Man page
addDiffMethTable Man page
addDiffMethTable,RnBDiffMeth-method Man page
add.error.plot Man page
addPheno Man page
addPheno,RnBSet-method Man page
add.quantile.plot Man page
addRegionSubsegments Man page
age.anti.transformation Man page
agePredictor Man page
agePredictor450 Man page
agePredictorRRBS Man page
age.transformation Man page
annotation Man page
annotation,RnBSet-method Man page
as.RnBeadRawSet Man page
assembly Man page
assembly,RnBSet-method Man page
auto.select.rank.cut Man page
BMIQ Man page
ClusterArchitecture-class Man page
ClusterArchitectureSGE-class Man page
coercion-methods Man page
combine.diffMeth.objs Man page
combine,RnBSet-method Man page
combine,RnBSet,RnBSet-method Man page
combineTestPvalsMeth Man page
computeDiffTab.default.region Man page
computeDiffTab.default.site Man page
computeDiffTab.extended.site Man page
computeDiffTab.region Man page
computeDiffTab.site Man page
covg Man page
covg,RnBSet-method Man page
create.densityScatter Man page
create.hex.summary.plot Man page
createPredictor Man page
createReport Man page
createReportGgPlot Man page
createReportPlot Man page
create.scatter.dens.points Man page
current Man page
cv.array Man page
cv.biseq Man page
data.frame2GRanges Man page
densRanks Man page
destroy Man page
destroy,RnBDiffMeth-method Man page
destroy,RnBeadRawSet-method Man page
destroy,RnBeadSet-method Man page
destroy,RnBSet-method Man page
deviation.plot.beta Man page
dpval Man page
dpval,RnBeadSet-method Man page
estimateProportionsCP Man page
exportDMRs2regionFile Man page
general.cv Man page
get.adjustment.variables Man page
get.comparison.grouplabels Man page
get.comparison.grouplabels,RnBDiffMeth-method Man page
get.comparison.groupsizes Man page
get.comparison.groupsizes,RnBDiffMeth-method Man page
get.comparison.info Man page
get.comparisons Man page
get.comparisons,RnBDiffMeth-method Man page
get.covariates.ct Man page
get.covariates.sva Man page
get.covg.thres Man page
get.covg.thres,RnBDiffMeth-method Man page
get.cpg.stats Man page
getExecutable Man page
getExecutable,ClusterArchitecture,character-method Man page
get.files Man page
getModuleNumCores Man page
getModuleNumCores,RnBClusterRun-method Man page
get.region.types Man page
get.region.types,RnBDiffMeth-method Man page
get.site.test.method Man page
get.site.test.method,RnBDiffMeth-method Man page
getSubCmdStr Man page
getSubCmdStr,ClusterArchitecture-method Man page
getSubCmdTokens Man page
getSubCmdTokens,ClusterArchitecture-method Man page
getSubCmdTokens,ClusterArchitectureSGE-method Man page
get.table Man page
get.table,RnBDiffMeth-method Man page
greedycut.filter.matrix Man page
greedycut.get.statistics Man page
greedycut.get.submatrix Man page
has.covariates.ct Man page
has.covariates.sva Man page
hasCovg Man page
hasCovg,RnBSet-method Man page
imputeRRBS Man page
includes.sites Man page
includes.sites,RnBDiffMeth-method Man page
infos Man page
initialize,ClusterArchitecture-method Man page
initialize,ClusterArchitectureSGE-method Man page
initialize,ReportGgPlot-method Man page
initialize,Report-method Man page
initialize,ReportPlot-method Man page
initialize,RnBClusterRun-method Man page
initialize,RnBDiffMeth-method Man page
initialize,RnBeadClustering-method Man page
initialize,RnBeadRawSet-method Man page
initialize,RnBeadSet-method Man page
initialize,RnBiseqSet-method Man page
intensities.by.color Man page
is.valid Man page
is.valid,RnBDiffMeth-method Man page
join.diffMeth Man page
join.diffMeth,RnBDiffMeth,RnBDiffMeth-method Man page
limmaP Man page
load.region.subsegment.annotation Man page
load.rnb.diffmeth Man page
load.rnb.set Man page
logger.argument Man page
logger.close Man page
logger.completed Man page
logger.error Man page
logger.getfiles Man page
logger.info Man page
logger.isinitialized Man page
logger.machine.name Man page
logger.start Man page
logger.status Man page
logger.validate.file Man page
logger.warning Man page
M Man page
mergeSamples Man page
mergeSamples,RnBSet-method Man page
meth Man page
meth,RnBSet-method Man page
M,RnBeadRawSet-method Man page
mval Man page
mval,RnBSet-method Man page
nsites Man page
nsites,RnBSet-method Man page
off Man page
off,ReportGgPlot-method Man page
off,Report-method Man page
off,ReportPlot-method Man page
parallel.getNumWorkers Man page
parallel.isEnabled Man page
parallel.setup Man page
parallel.teardown Man page
performEnrichment.diffMeth Man page
performGOenrichment.diffMeth.entrez Man page
pheno Man page
pheno,RnBSet-method Man page
previous Man page
qc Man page
qc,RnBeadSet-method Man page
read.bed.files Man page
read.data.dir Man page
read.geo Man page
read.geo.parse.characteristics_ch1 Man page
read.GS.report Man page
read.idat.files Man page
read.idat.files2 Man page
read.sample.annotation Man page
read.single.bed Man page
refFreeEWASP Man page
regionMapping Man page
regionMapping,RnBSet-method Man page
regions Man page
regions,RnBSet-method Man page
reload Man page
reload,RnBDiffMeth-method Man page
remove.regions Man page
remove.regions,RnBSet-method Man page
remove.samples Man page
remove.samples,RnBeadRawSet-method Man page
remove.samples,RnBeadSet-method Man page
remove.samples,RnBSet-method Man page
remove.sites Man page
remove.sites,RnBeadRawSet-method Man page
remove.sites,RnBeadSet-method Man page
remove.sites,RnBSet-method Man page
Report-class Man page
ReportGgPlot-class Man page
ReportPlot-class Man page
rnb.add.figure Man page
rnb.add.list Man page
rnb.add.paragraph Man page
rnb.add.reference Man page
rnb.add.section Man page
rnb.add.table Man page
rnb.add.tables Man page
rnb.annotation2data.frame Man page
rnb.annotation.size Man page
rnb.beta2mval Man page
rnb.build.index Man page
rnb.call.destructor Man page
RnBClusterRun-class Man page
rnb.color.legends Man page
RnBDiffMeth-class Man page
RnBeadClustering-class Man page
RnBeadRawSet Man page
RnBeadRawSet-class Man page
RnBeads Man page
RnBeads.data Man page
RnBeadSet Man page
RnBeadSet-class Man page
RnBeads-package Man page
rnb.execute.age.prediction Man page
rnb.execute.batcheffects Man page
rnb.execute.batch.qc Man page
rnb.execute.clustering Man page
rnb.execute.clustering.all Man page
rnb.execute.computeDiffMeth Man page
rnb.execute.context.removal Man page
rnb.execute.cross.reactive.removal Man page
rnb.execute.ct.estimation Man page
rnb.execute.dreduction Man page
rnb.execute.export.csv Man page
rnb.execute.filter.summary Man page
rnb.execute.gender.prediction Man page
rnb.execute.greedycut Man page
rnb.execute.high.coverage.removal Man page
rnb.execute.import Man page
rnb.execute.low.coverage.masking Man page
rnb.execute.na.removal Man page
rnb.execute.normalization Man page
rnb.execute.quality Man page
rnb.execute.sex.removal Man page
rnb.execute.snp.removal Man page
rnb.execute.sva Man page
rnb.execute.tnt Man page
rnb.execute.training Man page
rnb.execute.variability.removal Man page
rnb.export.all.annotation Man page
rnb.export.annotation Man page
rnb.export.to.ewasher Man page
rnb.export.to.trackhub Man page
rnb.find.relative.site.coord Man page
rnb.get.annotation Man page
rnb.get.assemblies Man page
rnb.get.chromosomes Man page
rnb.get.directory Man page
rnb.get.mapping Man page
rnb.getOption Man page
rnb.get.reference Man page
rnb.get.reliability.matrix Man page
rnb.infinium.control.targets Man page
rnb.initialize.reports Man page
RnBiseqSet Man page
RnBiseqSet-class Man page
rnb.is.option Man page
rnb.load.annotation Man page
rnb.load.sitelist Man page
rnb.message.plot Man page
rnb.mval2beta Man page
rnb.options Man page
rnb.options2xml Man page
rnb.performance.profile Man page
rnb.plot.beta.comparison Man page
rnb.plot.betadistribution.probeCategories Man page
rnb.plot.betadistribution.sampleGroups Man page
rnb.plot.biseq.coverage Man page
rnb.plot.biseq.coverage.hist Man page
rnb.plot.biseq.coverage.violin Man page
rnb.plot.control.barplot Man page
rnb.plot.control.boxplot Man page
rnb.plot.coverage.thresholds Man page
rnb.plot.ct.heatmap Man page
rnb.plot.dreduction Man page
rnb.plot.locus.profile Man page
rnb.plot.marker.fstat Man page
rnb.plot.negative.boxplot Man page
rnb.plot.num.sites.covg Man page
rnb.plot.pheno.categories Man page
rnb.plot.region.profile.density Man page
rnb.plot.region.profiles Man page
rnb.plot.region.site.density Man page
rnb.plot.sentrix.distribution Man page
rnb.plot.sentrix.distributions Man page
rnb.plot.snp.barplot Man page
rnb.plot.snp.boxplot Man page
rnb.plot.snp.heatmap Man page
rnb.region.types Man page
rnb.region.types.for.analysis Man page
rnb.remove.annotation Man page
rnb.RnBSet.to.bed Man page
rnb.RnBSet.to.bedGraph Man page
rnb.RnBSet.to.GRangesList Man page
rnb.run.analysis Man page
rnb.run.differential Man page
rnb.run.example Man page
rnb.run.exploratory Man page
rnb.run.import Man page
rnb.run.inference Man page
rnb.run.preprocessing Man page
rnb.run.qc Man page
rnb.run.tnt Man page
rnb.run.xml Man page
rnb.sample.groups Man page
rnb.sample.replicates Man page
rnb.sample.summary.table Man page
rnb.sample.summary.table,RnBSet-method Man page
rnb.save.annotation Man page
rnb.section.ageprediction Man page
rnb.set.annotation Man page
rnb.set.annotation.and.cpg.stats Man page
RnBSet-class Man page
rnb.show.report Man page
rnb.step.ageprediction Man page
rnb.step.betadistribution Man page
rnb.write.table Man page
rnb.xml2options Man page
rowOneSampleTP Man page
rowPairedTP Man page
rowWelchP Man page
run Man page
run.cross.validation Man page
run,RnBClusterRun-method Man page
sampleCovgApply Man page
sampleCovgApply,RnBSet-method Man page
sampleMethApply Man page
sampleMethApply,RnBSet-method Man page
samples Man page
samples,RnBeadClustering-method Man page
samples,RnBSet-method Man page
save.rnb.diffmeth Man page
save.rnb.set Man page
save.tables Man page
save.tables,RnBDiffMeth-method Man page
set.covariates.ct Man page
set.covariates.sva Man page
setExecutable Man page
setExecutable,ClusterArchitecture,character,character-method Man page
setModuleNumCores Man page
setModuleNumCores,RnBClusterRun,integer,character-method Man page
setModuleResourceRequirements Man page
setModuleResourceRequirements,RnBClusterRun,character,character- Man page
simpleGlmnet Man page
simpleGlmnetEvaluate Man page
simpleGlmnetRRBS Man page
sites Man page
sites,RnBSet-method Man page
summarized.regions Man page
summarized.regions,RnBSet-method Man page
summarize.regions Man page
summarize.regions,RnBSet-method Man page
trainPredictor Man page
U Man page
updateRegionSummaries Man page
updateRegionSummaries,RnBSet-method Man page
U,RnBeadRawSet-method Man page
writePredictorToCsv Man page

Files

RnBeads/BinaryFiles
RnBeads/DESCRIPTION
RnBeads/NAMESPACE
RnBeads/R
RnBeads/R/CNV.R RnBeads/R/Report-class.R RnBeads/R/Report-methods.R RnBeads/R/ReportPlot-class.R RnBeads/R/ReportPlot-methods.R RnBeads/R/RnBDiffMeth-class.R RnBeads/R/RnBSet-class.R RnBeads/R/RnBeadRawSet-class.R RnBeads/R/RnBeadSet-class.R RnBeads/R/RnBeads-package.R RnBeads/R/RnBiseqSet-class.R RnBeads/R/agePrediction.R RnBeads/R/annotations.R RnBeads/R/batch.R RnBeads/R/batch.quality.R RnBeads/R/bigFf.R RnBeads/R/bmiq.R RnBeads/R/cellTypeAdjustment.R RnBeads/R/clusterArchitecture.R RnBeads/R/clusterArchitectureSGE.R RnBeads/R/clustering.R RnBeads/R/computeCluster.R RnBeads/R/controlPlots.R RnBeads/R/controlPlotsBiSeq.R RnBeads/R/dataExport.R RnBeads/R/dataImport.R RnBeads/R/differentialMethylation.R RnBeads/R/enrichment.R RnBeads/R/filtering.R RnBeads/R/filteringSummary.R RnBeads/R/gender.R RnBeads/R/greedycut.R RnBeads/R/loading.R RnBeads/R/logger.R RnBeads/R/main.R RnBeads/R/normalization.R RnBeads/R/options.R RnBeads/R/parallelProcessing.R RnBeads/R/plottingUtils.R RnBeads/R/profiles.R RnBeads/R/qualityControl.R RnBeads/R/readGEO.R RnBeads/R/regionDescription.R RnBeads/R/regionProfiles.R RnBeads/R/subSegments.R RnBeads/R/sva.R RnBeads/R/utilities.R RnBeads/R/wbcInference.R
RnBeads/README
RnBeads/build
RnBeads/build/vignette.rds
RnBeads/data
RnBeads/inst
RnBeads/inst/CITATION
RnBeads/inst/NEWS
RnBeads/inst/bin
RnBeads/inst/bin/linux_x86.64
RnBeads/inst/bin/linux_x86.64/bedGraphToBigWig
RnBeads/inst/bin/linux_x86.64/bedToBigBed
RnBeads/inst/bin/macOSX.i386
RnBeads/inst/bin/macOSX.i386/bedGraphToBigWig
RnBeads/inst/bin/macOSX.i386/bedToBigBed
RnBeads/inst/doc
RnBeads/inst/doc/RnBeads.R
RnBeads/inst/doc/RnBeads.Rnw
RnBeads/inst/doc/RnBeads.pdf
RnBeads/inst/doc/RnBeads_Annotations.R
RnBeads/inst/doc/RnBeads_Annotations.Rnw
RnBeads/inst/doc/RnBeads_Annotations.pdf
RnBeads/inst/extdata
RnBeads/inst/extdata/RnBeads.png
RnBeads/inst/extdata/Rscript
RnBeads/inst/extdata/Rscript/rscript_differential.R
RnBeads/inst/extdata/Rscript/rscript_differential_chunk.R
RnBeads/inst/extdata/Rscript/rscript_differential_wrapup.R
RnBeads/inst/extdata/Rscript/rscript_exploratory.R
RnBeads/inst/extdata/Rscript/rscript_import.R
RnBeads/inst/extdata/Rscript/rscript_inference.R
RnBeads/inst/extdata/Rscript/rscript_preprocessing.R
RnBeads/inst/extdata/Rscript/rscript_qc.R
RnBeads/inst/extdata/Rscript/rscript_tnt.R
RnBeads/inst/extdata/Rscript/rscript_wrapup.R
RnBeads/inst/extdata/arrow_down.png
RnBeads/inst/extdata/arrow_right.png
RnBeads/inst/extdata/chromSizes
RnBeads/inst/extdata/chromSizes/hg19.chrom.sizes
RnBeads/inst/extdata/chromSizes/hg38.chrom.sizes
RnBeads/inst/extdata/chromSizes/mm10.chrom.sizes
RnBeads/inst/extdata/chromSizes/mm9.chrom.sizes
RnBeads/inst/extdata/chromSizes/rn5.chrom.sizes
RnBeads/inst/extdata/dna.png
RnBeads/inst/extdata/optionProfiles
RnBeads/inst/extdata/optionProfiles/450k_full.xml
RnBeads/inst/extdata/optionProfiles/450k_minimal.xml
RnBeads/inst/extdata/optionProfiles/450k_moderate.xml
RnBeads/inst/extdata/optionProfiles/bs_full.xml
RnBeads/inst/extdata/optionProfiles/bs_minimal.xml
RnBeads/inst/extdata/optionProfiles/bs_moderate.xml
RnBeads/inst/extdata/options.txt
RnBeads/inst/extdata/pdf_active.png
RnBeads/inst/extdata/pdf_inactive.png
RnBeads/inst/extdata/predefined_predictor_27K.csv
RnBeads/inst/extdata/predefined_predictor_450K.csv
RnBeads/inst/extdata/predefined_predictor_RRBS_hg19.csv
RnBeads/inst/extdata/predefined_predictor_RRBS_hg38.csv
RnBeads/inst/extdata/report.css
RnBeads/inst/extdata/report.js
RnBeads/inst/extdata/reportDescriptions.txt
RnBeads/inst/unitTests
RnBeads/inst/unitTests/dataset_generator.R
RnBeads/inst/unitTests/test_differential.R
RnBeads/inst/unitTests/test_logger.R
RnBeads/inst/unitTests/test_report_1.R
RnBeads/inst/unitTests/test_report_2.R
RnBeads/inst/unitTests/test_report_3.R
RnBeads/man
RnBeads/man/BMIQ.Rd RnBeads/man/ClusterArchitecture-class.Rd RnBeads/man/ClusterArchitectureSGE-class.Rd RnBeads/man/M-methods.Rd RnBeads/man/Report-class.Rd RnBeads/man/ReportGgPlot-class.Rd RnBeads/man/ReportPlot-class.Rd RnBeads/man/RnBClusterRun-class.Rd RnBeads/man/RnBDiffMeth-class.Rd RnBeads/man/RnBSet-class.Rd RnBeads/man/RnBeadClustering-class.Rd RnBeads/man/RnBeadRawSet-class.Rd RnBeads/man/RnBeadSet-class.Rd RnBeads/man/RnBeads.Rd RnBeads/man/RnBeads.data.Rd RnBeads/man/RnBiseqSet-class.Rd RnBeads/man/U-methods.Rd RnBeads/man/accepted.Rd RnBeads/man/add.age.histogram.Rd RnBeads/man/add.agecomparison.plot.Rd RnBeads/man/add.combination.plot.Rd RnBeads/man/add.error.plot.Rd RnBeads/man/add.quantile.plot.Rd RnBeads/man/addDiffMethTable-RnBDiffMeth-methods.Rd RnBeads/man/addPheno-RnBSet-methods.Rd RnBeads/man/addRegionSubsegments.Rd RnBeads/man/age.anti.transformation.Rd RnBeads/man/age.transformation.Rd RnBeads/man/agePredictor.Rd RnBeads/man/agePredictor450.Rd RnBeads/man/agePredictorRRBS.Rd RnBeads/man/annotation-methods.Rd RnBeads/man/as.RnBeadRawSet.Rd RnBeads/man/assembly-methods.Rd RnBeads/man/auto.select.rank.cut.Rd RnBeads/man/coercion-methods.Rd RnBeads/man/combine-methods.Rd RnBeads/man/combine.diffMeth.objs.Rd RnBeads/man/combineTestPvalsMeth.Rd RnBeads/man/computeDiffTab.region.Rd RnBeads/man/computeDiffTab.site.Rd RnBeads/man/covg-methods.Rd RnBeads/man/create.densityScatter.Rd RnBeads/man/create.hex.summary.plot.Rd RnBeads/man/create.scatter.dens.points.Rd RnBeads/man/createPredictor.Rd RnBeads/man/createReport.Rd RnBeads/man/createReportGgPlot.Rd RnBeads/man/createReportPlot.Rd RnBeads/man/cv.array.Rd RnBeads/man/cv.biseq.Rd RnBeads/man/data.frame2GRanges.Rd RnBeads/man/densRanks.Rd RnBeads/man/destroy-RnBDiffMeth-methods.Rd RnBeads/man/destroy-methods.Rd RnBeads/man/deviation.plot.beta.Rd RnBeads/man/dpval-methods.Rd RnBeads/man/estimateProportionsCP.Rd RnBeads/man/exportDMRs2regionFile.Rd RnBeads/man/general.cv.Rd RnBeads/man/get.adjustment.variables.Rd RnBeads/man/get.comparison.grouplabels-RnBDiffMeth-methods.Rd RnBeads/man/get.comparison.groupsizes-RnBDiffMeth-methods.Rd RnBeads/man/get.comparison.info.Rd RnBeads/man/get.comparisons-RnBDiffMeth-methods.Rd RnBeads/man/get.covariates.ct.Rd RnBeads/man/get.covariates.sva.Rd RnBeads/man/get.covg.thres-RnBDiffMeth-methods.Rd RnBeads/man/get.cpg.stats.Rd RnBeads/man/get.files.Rd RnBeads/man/get.region.types-RnBDiffMeth-methods.Rd RnBeads/man/get.site.test.method-RnBDiffMeth-methods.Rd RnBeads/man/get.table-RnBDiffMeth-methods.Rd RnBeads/man/getExecutable-ClusterArchitecture-methods.Rd RnBeads/man/getModuleNumCores-RnBClusterRun-methods.Rd RnBeads/man/getSubCmdStr-ClusterArchitecture-methods.Rd RnBeads/man/getSubCmdTokens-ClusterArchitecture-methods.Rd RnBeads/man/getSubCmdTokens-ClusterArchitectureSGE-methods.Rd RnBeads/man/greedycut.filter.matrix.Rd RnBeads/man/greedycut.get.statistics.Rd RnBeads/man/greedycut.get.submatrix.Rd RnBeads/man/has.covariates.ct.Rd RnBeads/man/has.covariates.sva.Rd RnBeads/man/hasCovg-methods.Rd RnBeads/man/imputeRRBS.Rd RnBeads/man/includes.sites-RnBDiffMeth-methods.Rd RnBeads/man/initialize-ClusterArchitecture-method.Rd RnBeads/man/initialize-ClusterArchitectureSGE-method.Rd RnBeads/man/initialize-RnBClusterRun-method.Rd RnBeads/man/initialize-RnBDiffMeth-method.Rd RnBeads/man/intensities.by.color.Rd RnBeads/man/is.valid-RnBDiffMeth-methods.Rd RnBeads/man/join.diffMeth-methods.Rd RnBeads/man/limmaP.Rd RnBeads/man/load.region.subsegment.annotation.Rd RnBeads/man/load.rnb.diffmeth.Rd RnBeads/man/load.rnb.set.Rd RnBeads/man/logger.argument.Rd RnBeads/man/logger.getfiles.Rd RnBeads/man/logger.isinitialized.Rd RnBeads/man/logger.machine.name.Rd RnBeads/man/logger.validate.file.Rd RnBeads/man/loggerManagement.Rd RnBeads/man/loggerMessages.Rd RnBeads/man/mergeSamples-methods.Rd RnBeads/man/meth-methods.Rd RnBeads/man/mval-methods.Rd RnBeads/man/nsites-methods.Rd RnBeads/man/off-methods.Rd RnBeads/man/parallel.getNumWorkers.Rd RnBeads/man/parallel.isEnabled.Rd RnBeads/man/parallel.setup.Rd RnBeads/man/parallel.teardown.Rd RnBeads/man/performEnrichment.diffMeth.Rd RnBeads/man/performGOenrichment.diffMeth.entrez.Rd RnBeads/man/pheno-methods.Rd RnBeads/man/qc-methods.Rd RnBeads/man/read.GS.report.Rd RnBeads/man/read.bed.files.Rd RnBeads/man/read.data.dir.Rd RnBeads/man/read.geo.Rd RnBeads/man/read.geo.parse.characteristics_ch1.Rd RnBeads/man/read.idat.files.Rd RnBeads/man/read.idat.files2.Rd RnBeads/man/read.sample.annotation.Rd RnBeads/man/read.single.bed.Rd RnBeads/man/refFreeEWASP.Rd RnBeads/man/regionMapping-methods.Rd RnBeads/man/regions-methods.Rd RnBeads/man/reload-RnBDiffMeth-methods.Rd RnBeads/man/remove.regions-methods.Rd RnBeads/man/remove.samples-methods.Rd RnBeads/man/remove.sites-methods.Rd RnBeads/man/rnb.RnBSet.to.GRangesList.Rd RnBeads/man/rnb.RnBSet.to.bed.Rd RnBeads/man/rnb.RnBSet.to.bedGraph.Rd RnBeads/man/rnb.add.figure.Rd RnBeads/man/rnb.add.list.Rd RnBeads/man/rnb.add.paragraph.Rd RnBeads/man/rnb.add.reference.Rd RnBeads/man/rnb.add.section.Rd RnBeads/man/rnb.add.table.Rd RnBeads/man/rnb.add.tables.Rd RnBeads/man/rnb.annotation.size.Rd RnBeads/man/rnb.annotation2data.frame.Rd RnBeads/man/rnb.beta2mval.Rd RnBeads/man/rnb.build.index.Rd RnBeads/man/rnb.call.destructor.Rd RnBeads/man/rnb.color.legends.Rd RnBeads/man/rnb.execute.age.prediction.Rd RnBeads/man/rnb.execute.batch.qc.Rd RnBeads/man/rnb.execute.batcheffects.Rd RnBeads/man/rnb.execute.clustering.Rd RnBeads/man/rnb.execute.clustering.all.Rd RnBeads/man/rnb.execute.computeDiffMeth.Rd RnBeads/man/rnb.execute.context.removal.Rd RnBeads/man/rnb.execute.cross.reactive.removal.Rd RnBeads/man/rnb.execute.ct.estimation.Rd RnBeads/man/rnb.execute.dreduction.Rd RnBeads/man/rnb.execute.export.csv.Rd RnBeads/man/rnb.execute.filter.summary.Rd RnBeads/man/rnb.execute.gender.prediction.Rd RnBeads/man/rnb.execute.greedycut.Rd RnBeads/man/rnb.execute.high.coverage.removal.Rd RnBeads/man/rnb.execute.import.Rd RnBeads/man/rnb.execute.low.coverage.masking.Rd RnBeads/man/rnb.execute.na.removal.Rd RnBeads/man/rnb.execute.normalization.Rd RnBeads/man/rnb.execute.quality.Rd RnBeads/man/rnb.execute.sex.removal.Rd RnBeads/man/rnb.execute.snp.removal.Rd RnBeads/man/rnb.execute.sva.Rd RnBeads/man/rnb.execute.tnt.Rd RnBeads/man/rnb.execute.training.Rd RnBeads/man/rnb.execute.variability.removal.Rd RnBeads/man/rnb.export.all.annotation.Rd RnBeads/man/rnb.export.annotation.Rd RnBeads/man/rnb.export.to.ewasher.Rd RnBeads/man/rnb.export.to.trackhub.Rd RnBeads/man/rnb.find.relative.site.coord.Rd RnBeads/man/rnb.get.annotation.Rd RnBeads/man/rnb.get.assemblies.Rd RnBeads/man/rnb.get.chromosomes.Rd RnBeads/man/rnb.get.directory.Rd RnBeads/man/rnb.get.mapping.Rd RnBeads/man/rnb.get.reference.Rd RnBeads/man/rnb.get.reliability.matrix.Rd RnBeads/man/rnb.infinium.control.targets.Rd RnBeads/man/rnb.initialize.reports.Rd RnBeads/man/rnb.is.option.Rd RnBeads/man/rnb.load.annotation.Rd RnBeads/man/rnb.load.sitelist.Rd RnBeads/man/rnb.message.plot.Rd RnBeads/man/rnb.mval2beta.Rd RnBeads/man/rnb.options.Rd RnBeads/man/rnb.options2xml.Rd RnBeads/man/rnb.performance.profile.Rd RnBeads/man/rnb.plot.beta.comparison.Rd RnBeads/man/rnb.plot.betadistribution.probeCategories.Rd RnBeads/man/rnb.plot.betadistribution.sampleGroups.Rd RnBeads/man/rnb.plot.biseq.coverage.Rd RnBeads/man/rnb.plot.biseq.coverage.hist.Rd RnBeads/man/rnb.plot.biseq.coverage.violin.Rd RnBeads/man/rnb.plot.control.barplot.Rd RnBeads/man/rnb.plot.control.boxplot.Rd RnBeads/man/rnb.plot.coverage.thresholds.Rd RnBeads/man/rnb.plot.ct.heatmap.Rd RnBeads/man/rnb.plot.dreduction.Rd RnBeads/man/rnb.plot.locus.profile.Rd RnBeads/man/rnb.plot.marker.fstat.Rd RnBeads/man/rnb.plot.negative.boxplot.Rd RnBeads/man/rnb.plot.num.sites.covg.Rd RnBeads/man/rnb.plot.pheno.categories.Rd RnBeads/man/rnb.plot.region.profile.density.Rd RnBeads/man/rnb.plot.region.profiles.Rd RnBeads/man/rnb.plot.region.site.density.Rd RnBeads/man/rnb.plot.sentrix.distribution.Rd RnBeads/man/rnb.plot.sentrix.distributions.Rd RnBeads/man/rnb.plot.snp.barplot.Rd RnBeads/man/rnb.plot.snp.boxplot.Rd RnBeads/man/rnb.plot.snp.heatmap.Rd RnBeads/man/rnb.region.types.Rd RnBeads/man/rnb.region.types.for.analysis.Rd RnBeads/man/rnb.remove.annotation.Rd RnBeads/man/rnb.run.analysis.Rd RnBeads/man/rnb.run.example.Rd RnBeads/man/rnb.run.xml.Rd RnBeads/man/rnb.runs.Rd RnBeads/man/rnb.sample.groups.Rd RnBeads/man/rnb.sample.replicates.Rd RnBeads/man/rnb.sample.summary.table.Rd RnBeads/man/rnb.save.annotation.Rd RnBeads/man/rnb.section.ageprediction.Rd RnBeads/man/rnb.set.annotation.Rd RnBeads/man/rnb.set.annotation.and.cpg.stats.Rd RnBeads/man/rnb.show.report.Rd RnBeads/man/rnb.step.ageprediction.Rd RnBeads/man/rnb.step.betadistribution.Rd RnBeads/man/rnb.write.table.Rd RnBeads/man/rnb.xml2options.Rd RnBeads/man/rowOneSampleTP.Rd RnBeads/man/rowPairedTP.Rd RnBeads/man/rowWelchP.Rd RnBeads/man/run-RnBClusterRun-methods.Rd RnBeads/man/run.cross.validation.Rd RnBeads/man/sampleCovgApply-methods.Rd RnBeads/man/sampleMethApply-methods.Rd RnBeads/man/samples-methods.Rd RnBeads/man/save.rnb.diffmeth.Rd RnBeads/man/save.rnb.set.Rd RnBeads/man/save.tables-RnBDiffMeth-methods.Rd RnBeads/man/set.covariates.ct.Rd RnBeads/man/set.covariates.sva.Rd RnBeads/man/setExecutable-ClusterArchitecture-methods.Rd RnBeads/man/setModuleNumCores-RnBClusterRun-methods.Rd RnBeads/man/setModuleResourceRequirements-RnBClusterRun-methods.Rd RnBeads/man/simpleGlmnet.Rd RnBeads/man/simpleGlmnetEvaluate.Rd RnBeads/man/simpleGlmnetRRBS.Rd RnBeads/man/sites-methods.Rd RnBeads/man/summarize.regions-methods.Rd RnBeads/man/summarized.regions-methods.Rd RnBeads/man/trainPredictor.Rd RnBeads/man/updateRegionSummaries.Rd RnBeads/man/writePredictorToCsv.Rd
RnBeads/tests
RnBeads/tests/runTests.R
RnBeads/vignettes
RnBeads/vignettes/RnBeads.Rnw
RnBeads/vignettes/RnBeads_Annotations.Rnw
RnBeads/vignettes/figures
RnBeads/vignettes/figures/beta_density.pdf
RnBeads/vignettes/figures/control_barplot_bad_conversion.pdf
RnBeads/vignettes/figures/control_boxplot_bad_conversion.pdf
RnBeads/vignettes/figures/deviationPlot_probeType.pdf
RnBeads/vignettes/figures/diffmeth_density_scatter.png
RnBeads/vignettes/figures/dreduction_custom.pdf
RnBeads/vignettes/figures/genomic_covg_plot.pdf
RnBeads/vignettes/figures/increases_gender.pdf
RnBeads/vignettes/figures/locusProfile_hoxd3.pdf
RnBeads/vignettes/figures/mds_sampleGroup.pdf
RnBeads/vignettes/figures/promoter_heatmap.pdf
RnBeads/vignettes/figures/rnbeads_workflow.pdf
RnBeads/vignettes/figures/snp_boxplot.png
RnBeads/vignettes/figures/snp_heatmap.pdf
RnBeads/vignettes/figures/sva_adj_pval_qqplot.pdf
RnBeads/vignettes/figures/volcanoDMRs_promoter.png

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