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

Files in this package

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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