API for RnBeads
RnBeads

Global functions
BMIQ Man page Source code
BigFfMat Source code
ClusterArchitecture-class Man page
ClusterArchitectureSGE-class Man page
HM27.snp.betas Source code
M Man page
M,RnBeadRawSet-method Man page
MethyLumiSet2RnBeadSet Source code
Report-class Man page
ReportGgPlot-class Man page
ReportPlot-class Man page
RnBClusterRun-class Man page
RnBDiffMeth-class Man page
RnBSet-class Man page
RnBeadClustering-class Man page
RnBeadRawSet Man page Source code
RnBeadRawSet-class Man page
RnBeadSet Man page Source code
RnBeadSet-class Man page
RnBeads Man page
RnBeads-package Man page
RnBeads.data Man page
RnBiseqSet Man page Source code
RnBiseqSet-class Man page
U Man page
U,RnBeadRawSet-method Man page
[,BigFfMat,ANY,ANY,ANY-method Man page
[<-,BigFfMat,ANY,ANY,ANY-method Man page
abbreviate.names Source code
accepted Man page
add.age.histogram Source code
add.agecomparison.plot Source code
add.combination.plot Source code
add.error.plot Source code
add.negative.control.boxplot Source code
add.profile.plots Source code
add.qc.barplots Source code
add.qc.boxplots Source code
add.quantile.plot Source code
add.seq.coverage.histograms Source code
add.seq.coverage.num.sites.covg.tabs Source code
add.seq.coverage.plot Source code
add.seq.coverage.violins Source code
add.subsegment.annotation Source code
add.text.subsampling Source code
addDiffMethTable Man page
addDiffMethTable,RnBDiffMeth-method Man page
addPheno Man page
addPheno,RnBSet-method Man page
addRegionSubsegments Man page Source code
addReportPlots.diffMeth.bin.region.scatter Source code
addReportPlots.diffMeth.bin.region.volcano Source code
addReportPlots.diffMeth.bin.site.scatter Source code
addReportPlots.diffMeth.bin.site.volcano Source code
addReportPlots.diffMeth.enrich.GO.wordcloud Source code
age.anti.transformation Source code
age.transformation Source code
agePredictor Source code
agePredictorBiseq Source code
agePredictorChip Source code
annotation Man page
annotation,RnBSet-method Man page
append.cpg.stats Source code
as.RnBeadRawSet Man page
assembly Man page
assembly,RnBSet-method Man page
auto.select.rank.cut Man page Source code
beta.value Source code
betaEst2 Source code
blc2 Source code
bootInferWBCbyLm Source code
bootInferWBCbyLme Source code
capitalize Source code
check.barcode Source code
check.idat.subdirs Source code
check.rnb.biseq.set Source code
coercion-methods Man page
colorize.value Source code
combine,RnBSet,RnBSet-method Man page
combine,RnBSet-method Man page
combine.diffMeth.objs Man page Source code
combine.sites Source code
combineTestPvalsMeth Man page Source code
combinedRanking.tab Source code
complete.report Source code
compute.sva.assoc Source code
computeDiffMeth.bin.region Source code
computeDiffMeth.bin.site Source code
computeDiffTab.default.region Man page Source code
computeDiffTab.default.site Man page Source code
computeDiffTab.extended.site Man page Source code
computeDiffTab.region Man page
computeDiffTab.site Man page
convert.string.ages Source code
convert.to.ff.matrix.tmp Source code
convert.to.ff.matrix.tmp2 Source code
covg Man page
covg,RnBSet-method Man page
create.densityScatter Man page Source code
create.diffMeth.bin.dens.dmp.scatter Source code
create.diffMeth.bin.dens.dmr.scatter Source code
create.empty.ff.matrix.tmp Source code
create.hex.summary.plot Man page Source code
create.path Source code
create.scatter.dens.points Man page Source code
create.ucsc.track.hub Source code
createPredictor Source code
createReport Man page Source code
createReportGgPlot Man page Source code
createReportPlot Man page Source code
current Man page
cv.array Source code
cv.biseq Source code
data.frame2GRanges Man page Source code
densRanks Man page Source code
destroy Man page
destroy,RnBDiffMeth-method Man page
destroy,RnBSet-method Man page
destroy,RnBeadRawSet-method Man page
destroy,RnBeadSet-method Man page
deviation.plot Source code
deviation.plot.beta Man page Source code
deviation.plot.beta.get.cuts Source code
deviation.plot.beta.internal Source code
dim,BigFfMat-method Man page
dist.correlation Source code
doPerm Source code
dpval Man page
dpval,RnBeadSet-method Man page
estimateProportionsCP Man page Source code
exportDMRs2regionFile Man page Source code
extractRankingCols.region Source code
extractRankingCols.site Source code
find.bed.column Source code
format.usage Source code
general.cv Source code
get.adjustment.variables Man page Source code
get.bed.column.classes Source code
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 Source code
get.comparisons Man page
get.comparisons,RnBDiffMeth-method Man page
get.components.isva Source code
get.components.sva Source code
get.covariates.ct Man page Source code
get.covariates.sva Man page Source code
get.covg.thres Man page
get.covg.thres,RnBDiffMeth-method Man page
get.cpg.stats Man page Source code
get.dataset.matrix Source code
get.density.dframe Source code
get.diffmeth.tab.annot.colnames.pretty Source code
get.diffmeth.tab.annot.cols Source code
get.diffmeth.tab.col.desc.list.txt Source code
get.disk.usage Source code
get.files Man page Source code
get.i.vector Source code
get.matrix.from.ff Source code
get.memory.usage Source code
get.methylation.color.panel Source code
get.pheno.tab Source code
get.region.types Man page
get.region.types,RnBDiffMeth-method Man page
get.relative.covg Source code
get.row.names Source code
get.silhouette Source code
get.site.and.region.types Source code
get.site.and.region.types.colors Source code
get.site.test.method Man page
get.site.test.method,RnBDiffMeth-method Man page
get.subsegments Source code
get.table Man page
get.table,RnBDiffMeth-method Man page
get.unified.scale Source code
getCGCounts Source code
getExecutable Man page
getExecutable,ClusterArchitecture,character-method Man page
getGLADProfiles Source code
getMergeList Source code
getModuleNumCores Man page
getModuleNumCores,RnBClusterRun-method Man page
getNumNaMeth Man page
getNumNaMeth,RnBSet-method Man page
getSubCmdStr Man page
getSubCmdStr,ClusterArchitecture-method Man page
getSubCmdTokens Man page
getSubCmdTokens,ClusterArchitecture-method Man page
getSubCmdTokens,ClusterArchitectureSGE-method Man page
greedycut.filter.matrix Man page Source code
greedycut.get.statistics Man page Source code
greedycut.get.submatrix Man page Source code
groupPermutationP.site Source code
groupPermutationP.site.parallel Source code
has.covariates.ct Man page Source code
has.covariates.sva Man page Source code
hasCovg Man page
hasCovg,RnBSet-method Man page
imputeBiseq Source code
includes.sites Man page
includes.sites,RnBDiffMeth-method Man page
index.list.2.factor Source code
inferWBCbyLm Source code
inferWBCbyLme Source code
infos Man page
init.pipeline.report Source code
initialize,ClusterArchitecture-method Man page
initialize,ClusterArchitectureSGE-method Man page
initialize,Report-method Man page
initialize,ReportGgPlot-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 Source code
intersect.elements Source code
is.valid Man page
is.valid,RnBDiffMeth-method Man page
is.valid.fname Source code
is.valid.permutations Source code
is.valid.relative Source code
join.diffMeth Man page
join.diffMeth,RnBDiffMeth,RnBDiffMeth-method Man page
limmaP Man page Source code
load.annotations Source code
load.bigFfMat Source code
load.region.subsegment.annotation Man page Source code
load.rnb.diffmeth Man page Source code
load.rnb.set Man page Source code
locus.profile.get.base.tracks Source code
locus.profile.get.methylation.track.heatmap Source code
locus.profile.get.methylation.track.param.processing Source code
locus.profile.get.methylation.track.smooth Source code
logger.addfile Source code
logger.argument Man page Source code
logger.close Man page Source code
logger.completed Man page Source code
logger.error Man page Source code
logger.format Source code
logger.getfiles Man page Source code
logger.info Man page Source code
logger.isinitialized Man page Source code
logger.machine.name Man page Source code
logger.paste Source code
logger.start Man page Source code
logger.status Man page Source code
logger.transform Source code
logger.validate.file Man page Source code
logger.warning Man page Source code
m.value Source code
mask.sites.meth Man page
mask.sites.meth,RnBSet-method Man page
match.chrom.names Source code
match.probes2annotation Source code
mds Source code
mergeColumns Source code
mergeSamples Man page
mergeSamples,RnBSet-method Man page
meth Man page
meth,RnBSet-method Man page
meth.matrices Source code
methylumi.intensities.by.color Source code
module.complete Source code
module.start.log Source code
mval Man page
mval,RnBSet-method Man page
nsites Man page
nsites,RnBSet-method Man page
off Man page
off,Report-method Man page
off,ReportGgPlot-method Man page
off,ReportPlot-method Man page
parallel.getNumWorkers Man page Source code
parallel.isEnabled Man page Source code
parallel.setup Man page Source code
parallel.teardown Man page Source code
parameter.is.flag Source code
parse.default Source code
parse.options Source code
performEnrichment.diffMeth Man page Source code
performGOenrichment.diffMeth.entrez Man page Source code
pheno Man page
pheno,RnBSet-method Man page
plot.heatmap.pc.correlations Source code
plot.heatmap.pc.pvalues Source code
plot.heatmap.rand Source code
plot.heatmap.symm Source code
plotCGHProfile Source code
plotcdf Source code
point.whisker.ggplot Source code
prepare.idat.dir Source code
prepare.slot.matrix Source code
previous Man page
print.inferWBC Source code
print.inferWBCBoot Source code
print.inferWBCsummary Source code
projectWBC Source code
qc Man page
qc,RnBeadSet-method Man page
read.GS.report Man page Source code
read.bed.files Man page Source code
read.data.dir Man page Source code
read.geo Man page Source code
read.geo.parse.characteristics_ch1 Man page Source code
read.idat.files Man page Source code
read.idat.files2 Man page Source code
read.sample.annotation Man page Source code
read.single.bed Man page Source code
refFreeEWASP Man page Source code
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,RnBSet-method Man page
remove.samples,RnBeadRawSet-method Man page
remove.samples,RnBeadSet-method Man page
remove.sites Man page
remove.sites,RnBSet-method Man page
remove.sites,RnBeadRawSet-method Man page
remove.sites,RnBeadSet-method Man page
rnb.RnBSet.to.GRangesList Man page Source code
rnb.RnBSet.to.bed Man page Source code
rnb.RnBSet.to.bedGraph Man page Source code
rnb.add.exported.tables Source code
rnb.add.figure Man page Source code
rnb.add.list Man page Source code
rnb.add.optionlist Source code
rnb.add.paragraph Man page Source code
rnb.add.reference Man page Source code
rnb.add.section Man page Source code
rnb.add.snp.barplot Source code
rnb.add.snp.boxplot Source code
rnb.add.snp.distances Source code
rnb.add.snp.heatmap Source code
rnb.add.snp.purity Source code
rnb.add.table Man page Source code
rnb.add.tables Man page Source code
rnb.annotation.size Man page Source code
rnb.annotation2data.frame Man page Source code
rnb.beta2mval Man page Source code
rnb.build.index Man page Source code
rnb.build.index.internal Source code
rnb.call.destructor Man page Source code
rnb.chromosome.lengths Source code
rnb.cleanMem Source code
rnb.color.legends Man page Source code
rnb.contains.sex Source code
rnb.convert.bed.to.bigBed Source code
rnb.convert.bedGraph.to.bigWig Source code
rnb.detect.infinium.platform Source code
rnb.diffmeth.to.EpiExplorer.file Source code
rnb.enmix.adjust Source code
rnb.enmix.cm Source code
rnb.enmix.em Source code
rnb.enmix.oob Source code
rnb.enmix.oob.sample Source code
rnb.error Source code
rnb.execute.age.prediction Man page Source code
rnb.execute.batch.qc Man page Source code
rnb.execute.batcheffects Man page Source code
rnb.execute.clustering Man page Source code
rnb.execute.clustering.all Man page Source code
rnb.execute.cnv Source code
rnb.execute.computeDiffMeth Man page Source code
rnb.execute.context.removal Man page Source code
rnb.execute.context.removal.internal Source code
rnb.execute.cross.reactive.removal Man page Source code
rnb.execute.cross.reactive.removal.internal Source code
rnb.execute.ct.estimation Man page Source code
rnb.execute.dreduction Man page Source code
rnb.execute.export.csv Man page Source code
rnb.execute.export.csv.save Source code
rnb.execute.filter.summary Man page Source code
rnb.execute.filter.summary.internal Source code
rnb.execute.gender.prediction Man page Source code
rnb.execute.greedycut Man page Source code
rnb.execute.greedycut.internal Source code
rnb.execute.high.coverage.removal Man page Source code
rnb.execute.high.coverage.removal.internal Source code
rnb.execute.import Man page Source code
rnb.execute.low.coverage.masking Man page Source code
rnb.execute.low.coverage.masking.internal Source code
rnb.execute.na.removal Man page Source code
rnb.execute.na.removal.internal Source code
rnb.execute.normalization Man page Source code
rnb.execute.normalization.bmiq Source code
rnb.execute.quality Man page Source code
rnb.execute.sex.removal Man page Source code
rnb.execute.sex.removal.internal Source code
rnb.execute.snp.removal Man page Source code
rnb.execute.snp.removal.internal Source code
rnb.execute.sva Man page Source code
rnb.execute.tnt Man page Source code
rnb.execute.training Man page Source code
rnb.execute.variability.removal Man page Source code
rnb.execute.variability.removal.internal Source code
rnb.export.all.annotation Man page Source code
rnb.export.annotation Man page Source code
rnb.export.fail Source code
rnb.export.to.ewasher Man page Source code
rnb.export.to.trackhub Man page Source code
rnb.filter.dataset Source code
rnb.filtering.results Source code
rnb.find.relative.site.coord Man page Source code
rnb.fix.strand Source code
rnb.get.XY.shifts Source code
rnb.get.annotation Man page Source code
rnb.get.assemblies Man page Source code
rnb.get.chromosomes Man page Source code
rnb.get.cnv.annotations Source code
rnb.get.cols Source code
rnb.get.covg.token Source code
rnb.get.directory Man page Source code
rnb.get.executable Source code
rnb.get.filtered.sites.samples Source code
rnb.get.mapping Man page Source code
rnb.get.option Source code
rnb.get.reference Man page Source code
rnb.get.reliability.counts.per.sample Source code
rnb.get.reliability.matrix Man page Source code
rnb.get.row.token Source code
rnb.get.sentrix.data Source code
rnb.get.snp.matrix Source code
rnb.getOption Man page Man page Source code
rnb.greedycut.table Source code
rnb.has.reliability.info Source code
rnb.infinium.control.targets Man page Source code
rnb.info Source code
rnb.initialize.reports Man page Source code
rnb.is.option Man page Source code
rnb.load.annotation Man page Source code
rnb.load.bed Source code
rnb.load.sitelist Man page Source code
rnb.logger.completed Source code
rnb.logger.start Source code
rnb.message.plot Man page Source code
rnb.mval2beta Man page Source code
rnb.options Man page Source code
rnb.options2xml Man page Source code
rnb.performance.profile Man page Source code
rnb.pheno2colors Source code
rnb.plot.GLAD.profile Source code
rnb.plot.beta.comparison Man page Source code
rnb.plot.beta.density.group Source code
rnb.plot.betadistribution.probeCategories Man page Source code
rnb.plot.betadistribution.sampleGroups Man page Source code
rnb.plot.biseq.coverage Man page Source code
rnb.plot.biseq.coverage.hist Man page Source code
rnb.plot.biseq.coverage.violin Man page Source code
rnb.plot.control.barplot Man page Source code
rnb.plot.control.boxplot Man page Source code
rnb.plot.coverage.thresholds Man page Source code
rnb.plot.ct.heatmap Man page Source code
rnb.plot.dreduction Man page Source code
rnb.plot.locus.profile Man page Source code
rnb.plot.marker.fstat Man page Source code
rnb.plot.negative.boxplot Man page Source code
rnb.plot.num.sites.covg Man page Source code
rnb.plot.pheno.categories Man page Source code
rnb.plot.region.profile.density Man page Source code
rnb.plot.region.profiles Man page Source code
rnb.plot.region.site.density Man page Source code
rnb.plot.sentrix.distribution Man page Source code
rnb.plot.sentrix.distributions Man page Source code
rnb.plot.snp.barplot Man page Source code
rnb.plot.snp.boxplot Man page Source code
rnb.plot.snp.heatmap Man page Source code
rnb.probe.types Source code
rnb.process.sitelist Source code
rnb.region.types Man page Source code
rnb.region.types.for.analysis Man page Source code
rnb.regions2sites Source code
rnb.remove.annotation Man page Source code
rnb.require Source code
rnb.run.analysis Man page Source code
rnb.run.differential Man page Source code
rnb.run.example Man page Source code
rnb.run.exploratory Man page Source code
rnb.run.import Man page Source code
rnb.run.inference Man page Source code
rnb.run.preprocessing Man page Source code
rnb.run.qc Man page Source code
rnb.run.tnt Man page Source code
rnb.run.xml Man page Source code
rnb.sample.groups Man page Source code
rnb.sample.replicates Man page Source code
rnb.sample.summary.table Man page Source code
rnb.sample.summary.table,RnBSet-method Man page
rnb.save.annotation Man page Source code
rnb.save.removed.sites Source code
rnb.section.ageprediction Source code
rnb.section.batch.qc Source code
rnb.section.batcheffects Source code
rnb.section.clustering Source code
rnb.section.clustering.add.heatmap Source code
rnb.section.cnv Source code
rnb.section.context.removal Source code
rnb.section.context.removal.internal Source code
rnb.section.cross.reactive.removal Source code
rnb.section.cross.reactive.removal.internal Source code
rnb.section.ct.estimation Source code
rnb.section.diffMeth.introduction Source code
rnb.section.diffMeth.region Source code
rnb.section.diffMeth.site Source code
rnb.section.dreduction Source code
rnb.section.dreduction.internal Source code
rnb.section.export.csv Source code
rnb.section.export.ct.adj Source code
rnb.section.gender.prediction Source code
rnb.section.high.coverage.removal Source code
rnb.section.high.coverage.removal.internal Source code
rnb.section.import Source code
rnb.section.locus.profiles Source code
rnb.section.low.coverage.masking Source code
rnb.section.low.coverage.masking.internal Source code
rnb.section.na.removal Source code
rnb.section.na.removal.internal Source code
rnb.section.normalization Source code
rnb.section.normalization.shifts Source code
rnb.section.normalize.regions Source code
rnb.section.quality Source code
rnb.section.region.description Source code
rnb.section.region.profiles Source code
rnb.section.region.subsegmentation Source code
rnb.section.replicate.concordance Source code
rnb.section.sample.groups Source code
rnb.section.sex.removal Source code
rnb.section.sex.removal.internal Source code
rnb.section.snp.probes Source code
rnb.section.snp.removal Source code
rnb.section.snp.removal.internal Source code
rnb.section.sva Source code
rnb.section.tnt Source code
rnb.section.variability.removal Source code
rnb.set.annotation Man page Source code
rnb.set.annotation.and.cpg.stats Man page Source code
rnb.set.update.predicted.gender Source code
rnb.show.report Man page Source code
rnb.show.rnbeadset Source code
rnb.sitelist.info Source code
rnb.sort.regions Source code
rnb.status Source code
rnb.step.ageprediction Source code
rnb.step.analyze.targets Source code
rnb.step.batch.qc Source code
rnb.step.batcheffects Source code
rnb.step.betadistribution Man page Source code
rnb.step.betadistribution.internal Source code
rnb.step.cell.types Source code
rnb.step.clustering Source code
rnb.step.clustering.internal Source code
rnb.step.cnv Source code
rnb.step.context.removal Source code
rnb.step.context.removal.internal Source code
rnb.step.cross.reactive.removal Source code
rnb.step.cross.reactive.removal.internal Source code
rnb.step.dreduction Source code
rnb.step.filter.summary Source code
rnb.step.filter.summary.internal Source code
rnb.step.gender.prediction Source code
rnb.step.greedycut Source code
rnb.step.greedycut.internal Source code
rnb.step.high.coverage.removal Source code
rnb.step.high.coverage.removal.internal Source code
rnb.step.import Source code
rnb.step.intersample Source code
rnb.step.intersample.internal Source code
rnb.step.locus.profiles Source code
rnb.step.low.coverage.masking Source code
rnb.step.low.coverage.masking.internal Source code
rnb.step.na.removal Source code
rnb.step.na.removal.internal Source code
rnb.step.normalization Source code
rnb.step.quality Source code
rnb.step.region.profiles Source code
rnb.step.region.subsegmentation Source code
rnb.step.sex.removal Source code
rnb.step.sex.removal.internal Source code
rnb.step.snp.probes Source code
rnb.step.snp.removal Source code
rnb.step.snp.removal.internal Source code
rnb.step.sva Source code
rnb.step.variability.removal Source code
rnb.step.variability.removal.internal Source code
rnb.tracks.to.export Source code
rnb.update.annotation.infos Source code
rnb.update.controlsEPIC.enrich Source code
rnb.validate.option Source code
rnb.validate.xml.option Source code
rnb.warning Source code
rnb.write.table Man page Source code
rnb.xml2options Man page Source code
rnbreport.create.settings.table Source code
rnbreport.get.element.values Source code
robustHyperGResultSummary Source code
rowOneSampleTP Man page Source code
rowPairedTP Man page Source code
rowWelchP Man page Source code
run Man page
run,RnBClusterRun-method Man page
run.cross.validation Man page Source code
sampleCovgApply Man page
sampleCovgApply,RnBSet-method Man page
sampleMethApply Man page
sampleMethApply,RnBSet-method Man page
samples Man page
samples,RnBSet-method Man page
samples,RnBeadClustering-method Man page
save.bigFfMat Source code
save.rnb.diffmeth Man page Source code
save.rnb.set Man page Source code
save.tables Man page
save.tables,RnBDiffMeth-method Man page
set.covariates.ct Man page Source code
set.covariates.sva Man page Source code
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 Source code
simpleGlmnetBiseq Source code
simpleGlmnetEvaluate Source code
sites Man page
sites,RnBSet-method Man page
sortAndExtendRegions Source code
summarize.bead.counts Source code
summarize.regions Man page
summarize.regions,RnBSet-method Man page
summarized.regions Man page
summarized.regions,RnBSet-method Man page
summary.inferWBC Source code
summary.inferWBCBoot Source code
symmetric.melt Source code
tTestP Source code
test.traits Source code
trainPredictor Source code
unload.annotations Source code
updateRegionSummaries Man page
updateRegionSummaries,RnBSet-method Man page
validRnBeadRawSetObject Source code
validRnBeadSetObject Source code
validate.dir Source code
validate.module.parameters Source code
validate.pcoordinates Source code
validate.pcoordinates.all Source code
validate.single Source code
validate.stats Source code
write.line Source code
write.table.options Source code
writePredictorToCsv Source code
RnBeads documentation built on May 31, 2017, 11:35 a.m.