Man pages for RnBeads
RnBeads
| accepted | RnBeads option values and restrictions |
| addDiffMethTable-RnBDiffMeth-methods | addDiffMethTable-methods |
| addPheno-RnBSet-methods | addPheno |
| addRegionSubsegments | addRegionSubsegments |
| annotation-methods | annotation-methods |
| apply.iEVORA | apply.iEVORA |
| as.RnBeadRawSet | Conversion to/from RnBeadRawSet |
| assembly-methods | assembly-methods |
| auto.select.rank.cut | auto.select.rank.cut |
| BMIQ | BMIQ |
| ClusterArchitecture-class | ClusterArchitecture Class |
| ClusterArchitectureSGE-class | ClusterArchitectureSGE Class |
| ClusterArchitectureSLURM-class | ClusterArchitectureSLURM Class |
| coercion-methods | as("RnBeadSet", "MethyLumiSet") |
| cols.to.rank | cols.to.rank.site |
| 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 |
| createReport | createReport |
| createReportGgPlot | createReportGgPlot |
| createReportPlot | createReportPlot |
| create.scatter.dens.points | create.scatter.dens.points |
| data.frame2GRanges | data.frame2GRanges |
| densRanks | densRanks |
| destroy-methods | destroy-methods |
| destroy-RnBDiffMeth-methods | destroy-methods |
| deviation.plot.beta | deviation.plot.beta |
| diffVar | diffVar |
| dim-BigFfMat-method | Dimensions of BigFfMat |
| downloadLolaDbs | downloadLolaDbs |
| dpval-methods | dpval-methods |
| estimateProportionsCP | estimateProportionsCP |
| exportDMRs2regionFile | exportDMRs2regionFile |
| get.adjustment.variables | get.adjustment.variables |
| getCellTypesFromLolaDb | getCellTypesFromLolaDb |
| 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 |
| getNamesFromLolaDb | getNamesFromLolaDb |
| getNumNaMeth-methods | getNumNaMeth-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 |
| getSubCmdTokens-ClusterArchitectureSLURM-methods | getSubCmdTokens-methods |
| get.table.ids | Returns the colum names of the differential variability... |
| get.table-RnBDiffMeth-methods | get.table-methods |
| getTargetFromLolaDb | getTargetFromLolaDb |
| get.variability.method-RnBDiffMeth-methods | get.variability.method-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 |
| includes.sites-RnBDiffMeth-methods | includes.sites-methods |
| initialize-ClusterArchitecture-method | initialize.ClusterArchitecture |
| initialize-ClusterArchitectureSGE-method | initialize.ClusterArchitectureSGE |
| initialize-ClusterArchitectureSLURM-method | initialize.ClusterArchitectureSLURM |
| initialize-RnBClusterRun-method | initialize.RnBClusterRun |
| initialize-RnBDiffMeth-method | initialize.RnBDiffMeth |
| intensities.by.color | intensities.by.color |
| isImputed-RnBSet-method | isImputed |
| is.valid-RnBDiffMeth-methods | is.valid-methods |
| join.diffMeth-methods | join.diffMeth-methods |
| limmaP | limmaP |
| loadLolaDbs | loadLolaDbs |
| 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 |
| lolaBarPlot | lolaBarPlot |
| lolaBoxPlotPerTarget | lolaBoxPlotPerTarget |
| lolaVolcanoPlot | lolaVolcanoPlot |
| lump.hg19 | LUMP Support |
| lump.hg38 | LUMP Support (hg38) |
| mask.sites.meth-methods | mask.sites.meth-methods |
| 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 |
| performGoEnrichment.diffMeth | performGoEnrichment.diffMeth |
| performGOenrichment.diffMeth.entrez | performGOenrichment.diffMeth.entrez |
| performGOEnrichment.diffVar | performGOEnrichment.diffVar |
| performLolaEnrichment.diffMeth | performLolaEnrichment.diffMeth |
| performLolaEnrichment.diffVar | performLolaEnrichment.diffVar |
| pheno-methods | pheno-methods |
| prepareSOFTfileForGEO | prepareSOFTfileForGEO |
| qc-methods | qc-methods |
| read.bed.files | read.bed.files |
| read.data.dir | read.data.dir |
| 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.bed.from.segmentation | rnb.bed.from.segmentation |
| rnb.beta2mval | rnb.beta2mval |
| rnb.boxplot.from.segmentation | rnb.boxplot.from.segmentation |
| rnb.build.index | rnb.build.index |
| rnb.call.destructor | rnb.call.destructor |
| RnBClusterRun-class | RnBClusterRun Class |
| rnb.color.legends | rnb.color.legends |
| rnb.combine.arrays | Combine array-based datasets |
| rnb.combine.seq | rnb.combine.seq |
| 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.diffVar | rnb.execute.diffVar |
| 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.genomewide | Genome-wide methylation level |
| rnb.execute.greedycut | rnb.execute.greedycut |
| rnb.execute.high.coverage.removal | rnb.execute.high.coverage.removal |
| rnb.execute.import | rnb.execute.import |
| rnb.execute.imputation | rnb.execute.imputation |
| rnb.execute.low.coverage.masking | rnb.execute.low.coverage.masking |
| rnb.execute.lump | Leukocytes unmethylation for purity |
| rnb.execute.na.removal | rnb.execute.na.removal |
| rnb.execute.normalization | rnb.execute.normalization |
| rnb.execute.quality | rnb.execute.quality |
| rnb.execute.segmentation | rnb.execute.segmentation |
| rnb.execute.sex.prediction | rnb.execute.sex.prediction |
| 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.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.annotation.from.db | rnb.load.annotation.from.db |
| 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.read.geo | Import methylation data from GEO |
| 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 | Export to BED files |
| rnb.RnBSet.to.bedGraph | rnb.RnBSet.to.bedGraph |
| rnb.RnBSet.to.GRangesList | rnb.RnBSet.to.GRangesList |
| rnb.run.analysis | RnBeads Analysis Pipeline |
| rnb.run.dj | rnb.run.dj |
| 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.diffVar.region | rnb.section.diffVar.region |
| 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.betadistribution | rnb.step.betadistribution |
| rnb.step.cnv | rnb.step.cnv |
| 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 |
| sites-methods | sites-methods |
| sub-BigFfMat-ANY-ANY-ANY-method | Extract parts of BigFfMat |
| subset-BigFfMat-ANY-ANY-ANY-method | Replace parts of BigFfMat |
| summarized.regions-methods | summarized.regions-methods |
| summarize.regions-methods | summarize.regions-methods |
| U-methods | U-methods |
| updateMethylationSites-methods | updateMethylationSites-methods |
| updateRegionSummaries | updateRegionSummaries |
