| BMIQ |
Man page
Source code
|
| BigFfMat |
Source code
|
| ClusterArchitecture-class |
Man page
|
| ClusterArchitectureSGE-class |
Man page
|
| ClusterArchitectureSLURM-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.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.stratification.plot |
Source code
|
| add.stratification.plot.immune |
Source code
|
| add.subsegment.annotation |
Source code
|
| addDiffMethTable |
Man page
|
| addDiffMethTable,RnBDiffMeth-method |
Man page
|
| addPheno |
Man page
|
| addPheno,RnBSet-method |
Man page
|
| addRegionSubsegments |
Man page
Source code
|
| addReportPlot.diffVar.meth |
Source code
|
| addReportPlot.diffVar.meth.region |
Source code
|
| addReportPlot.diffVar.volcano.region |
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
|
| apply.iEVORA |
Man page
Source code
|
| as.RnBeadRawSet |
Man page
|
| assembly |
Man page
|
| assembly,RnBSet-method |
Man page
|
| auto.select.rank.cut |
Man page
Source code
|
| basic_combine |
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
|
| cols.to.rank.region |
Man page
Source code
|
| cols.to.rank.site |
Man page
Source code
|
| combine |
Man page
|
| 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
|
| computeDiffVar.bin.region |
Source code
|
| computeDiffVar.bin.site |
Source code
|
| computeDiffVar.default.region |
Source code
|
| 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
|
| create.diffMeth.diffVar.subsample |
Source code
|
| create.empty.ff.matrix.tmp |
Source code
|
| create.hex.summary.plot |
Man page
|
| create.path |
Source code
|
| create.scatter.dens.points |
Man page
|
| 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
|
| 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.beta |
Man page
|
| diffVar |
Man page
Source code
|
| dim,BigFfMat-method |
Man page
|
| dist.correlation |
Source code
|
| doDV |
Source code
|
| doPerm |
Source code
|
| doTT |
Source code
|
| downloadLolaDbs |
Man page
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.table.ids |
Man page
Source code
|
| get.unified.scale |
Source code
|
| get.variability.method |
Man page
|
| get.variability.method,RnBDiffMeth-method |
Man page
|
| getCGCounts |
Source code
|
| getCellTypesFromLolaDb |
Man page
Source code
|
| getExecutable |
Man page
|
| getExecutable,ClusterArchitecture,character-method |
Man page
|
| getExecutable,ClusterArchitecture-method |
Man page
|
| getGLADProfiles |
Source code
|
| getMergeList |
Source code
|
| getModuleNumCores |
Man page
|
| getModuleNumCores,RnBClusterRun-method |
Man page
|
| getNamesFromLolaDb |
Man page
Source code
|
| getNumNaMeth |
Man page
|
| getNumNaMeth,RnBSet-method |
Man page
|
| getRoadmapMdFromId |
Source code
|
| getSubCmdStr |
Man page
|
| getSubCmdStr,ClusterArchitecture-method |
Man page
|
| getSubCmdTokens |
Man page
|
| getSubCmdTokens,ClusterArchitecture-method |
Man page
|
| getSubCmdTokens,ClusterArchitectureSGE-method |
Man page
|
| getSubCmdTokens,ClusterArchitectureSLURM-method |
Man page
|
| getTargetFromLolaDb |
Man page
Source code
|
| 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
|
| iEVORA |
Source code
|
| imputation.low.memory.cpgs |
Source code
|
| imputation.low.memory.samples |
Source code
|
| 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,ClusterArchitectureSLURM-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
|
| 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
|
| isImputed |
Man page
|
| isImputed,RnBSet-method |
Man page
|
| join.diffMeth |
Man page
|
| join.diffMeth,RnBDiffMeth,RnBDiffMeth-method |
Man page
|
| knn.imputation |
Source code
|
| 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
|
| loadLolaDbs |
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
|
| lolaBarPlot |
Man page
Source code
|
| lolaBarPlot.hyp |
Source code
|
| lolaBoxPlotPerTarget |
Man page
Source code
|
| lolaPrepareDataFrameForPlot |
Source code
|
| lolaVolcanoPlot |
Man page
Source code
|
| lump.hg19 |
Man page
|
| lump.hg38 |
Man page
|
| 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
|
| mean.imputation |
Source code
|
| median.imputation |
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
|
| performGOEnrichment.diffVar |
Man page
Source code
|
| performGOenrichment.diffMeth.entrez |
Man page
Source code
|
| performGoEnrichment.diffMeth |
Man page
Source code
|
| performLolaEnrichment.diffMeth |
Man page
Source code
|
| performLolaEnrichment.diffVar |
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
|
| point.whisker.ggplot |
Source code
|
| prepLolaDbPaths |
Source code
|
| prepare.idat.dir |
Source code
|
| prepare.slot.matrix |
Source code
|
| prepareGEOSampleInfoTemplate |
Source code
|
| prepareSOFTfileForGEO |
Man page
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
|
| random.imputation |
Source code
|
| read.GS.report |
Man page
Source code
|
| read.bed.files |
Man page
Source code
|
| read.data.dir |
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.bed.from.segmentation |
Man page
Source code
|
| rnb.beta2mval |
Man page
Source code
|
| rnb.boxplot.from.segmentation |
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
|
| rnb.combine.arrays |
Man page
Source code
|
| rnb.combine.matrices |
Source code
|
| rnb.combine.pheno |
Source code
|
| rnb.combine.seq |
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.diffVar |
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.genomewide |
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.imputation |
Man page
Source code
|
| rnb.execute.low.coverage.masking |
Man page
Source code
|
| rnb.execute.low.coverage.masking.internal |
Source code
|
| rnb.execute.lump |
Man page
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.segmentation |
Man page
Source code
|
| rnb.execute.sex.prediction |
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.final.segmentation |
Source code
|
| rnb.find.relative.site.coord |
Man page
Source code
|
| rnb.fix.strand |
Source code
|
| rnb.geo.init.matrix |
Source code
|
| rnb.geo.parse.ids |
Source code
|
| rnb.geo.parse.sample.anno |
Source code
|
| rnb.geo.parse.sample.info |
Source code
|
| rnb.geo.parse.series.matrix |
Source code
|
| rnb.get.XY.shifts |
Source code
|
| rnb.get.XY.shifts.biseq |
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
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.annotation.from.db |
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
|
| rnb.mval2beta |
Man page
Source code
|
| rnb.option.compatibility |
Source code
|
| rnb.options |
Man page
Source code
|
| rnb.options.description.table |
Source code
|
| rnb.options.description.table.fromRd |
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
|
| 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
|
| 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.segmentation.distributions |
Source code
|
| rnb.plot.segmentation.final |
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.read.geo |
Man page
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.dj |
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.diffVar |
Source code
|
| rnb.section.diffVar.region |
Man page
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.genomewide |
Source code
|
| rnb.section.high.coverage.removal |
Source code
|
| rnb.section.high.coverage.removal.internal |
Source code
|
| rnb.section.import |
Source code
|
| rnb.section.imputation |
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.lump |
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.prediction |
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.sex |
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 |
Man page
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.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.imputation |
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.prediction |
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
Source code
|
| 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
|
| setExecutable,ClusterArchitecture-method |
Man page
|
| setModuleNumCores |
Man page
|
| setModuleNumCores,RnBClusterRun,integer,character-method |
Man page
|
| setModuleNumCores,RnBClusterRun-method |
Man page
|
| setModuleResourceRequirements |
Man page
|
| setModuleResourceRequirements,RnBClusterRun,character,character- |
Man page
|
| setModuleResourceRequirements,RnBClusterRun-method |
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
|
| trimChar |
Source code
|
| unload.annotations |
Source code
|
| updateMethylationSites |
Man page
|
| updateMethylationSites,RnBSet-method |
Man page
|
| 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
|
