RnBeads: RnBeads

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

Author
Yassen Assenov [aut], Pavlo Lutsik [aut], Fabian Mueller [aut, cre]
Date of publication
None
Maintainer
Fabian Mueller <rnbeads@mpi-inf.mpg.de>
License
GPL-3
Version
1.6.1

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