RnBeads
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Documentation for package ‘RnBeads’ version 2.26.0
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A B C D E G H I J L M N O P Q R S U misc
| RnBeads-package | Analysis of genome-scale DNA methylation data with RnBeads |
-- A --
| accepted | RnBeads option values and restrictions |
| addDiffMethTable | addDiffMethTable-methods |
| addDiffMethTable-method | addDiffMethTable-methods |
| addPheno | addPheno |
| addPheno-method | addPheno |
| addRegionSubsegments | addRegionSubsegments |
| annotation | annotation-methods |
| annotation-method | annotation-methods |
| apply.iEVORA | apply.iEVORA |
| as.RnBeadRawSet | Conversion to/from RnBeadRawSet |
| assembly | assembly-methods |
| assembly-method | assembly-methods |
| auto.select.rank.cut | auto.select.rank.cut |
-- B --
| BMIQ | BMIQ |
-- C --
| ClusterArchitecture-class | ClusterArchitecture Class |
| ClusterArchitectureLSF-class | ClusterArchitectureLSF Class |
| ClusterArchitectureSGE-class | ClusterArchitectureSGE Class |
| ClusterArchitectureSLURM-class | ClusterArchitectureSLURM Class |
| coercion-methods | as("RnBeadSet", "MethyLumiSet") |
| cols.to.rank.region | cols.to.rank.site |
| cols.to.rank.site | cols.to.rank.site |
| combine.diffMeth.objs | combine.diffMeth.objs |
| combine.rnb.sets | combine.rnb.sets-methods |
| combine.rnb.sets-method | combine.rnb.sets-methods |
| combineTestPvalsMeth | combineTestPvalsMeth |
| computeDiffTab.default.region | computeDiffTab.region |
| computeDiffTab.default.site | computeDiffTab.site |
| computeDiffTab.extended.site | computeDiffTab.site |
| computeDiffTab.region | computeDiffTab.region |
| computeDiffTab.site | computeDiffTab.site |
| covg | covg-methods |
| covg-method | covg-methods |
| create.densityScatter | create.densityScatter |
| create.hex.summary.plot | create.hex.summary.plot |
| create.scatter.dens.points | create.scatter.dens.points |
| createReport | createReport |
| createReportGgPlot | createReportGgPlot |
| createReportPlot | createReportPlot |
| current | RnBeads option values and restrictions |
-- D --
| data.frame2GRanges | data.frame2GRanges |
| densRanks | densRanks |
| destroy | destroy-methods |
| destroy-method | destroy-methods |
| destroy-method | destroy-methods |
| deviation.plot.beta | deviation.plot.beta |
| diffVar | diffVar |
| dim-method | Dimensions of BigFfMat |
| downloadLolaDbs | downloadLolaDbs |
| dpval | dpval-methods |
| dpval-method | dpval-methods |
-- E --
| estimateProportionsCP | estimateProportionsCP |
| exportDMRs2regionFile | exportDMRs2regionFile |
-- G --
| get.adjustment.variables | get.adjustment.variables |
| get.comparison.grouplabels | get.comparison.grouplabels-methods |
| get.comparison.grouplabels-method | get.comparison.grouplabels-methods |
| get.comparison.groupsizes | get.comparison.groupsizes-methods |
| get.comparison.groupsizes-method | get.comparison.groupsizes-methods |
| get.comparison.info | get.comparison.info |
| get.comparisons | get.comparisons-methods |
| get.comparisons-method | get.comparisons-methods |
| get.covariates.ct | get.covariates.ct |
| get.covariates.sva | get.covariates.sva |
| get.covg.thres | get.covg.thres-methods |
| get.covg.thres-method | get.covg.thres-methods |
| get.cpg.stats | get.cpg.stats |
| get.files | get.files |
| get.region.types | get.region.types-methods |
| get.region.types-method | get.region.types-methods |
| get.site.test.method | get.site.test.method-methods |
| get.site.test.method-method | get.site.test.method-methods |
| get.table | get.table-methods |
| get.table-method | get.table-methods |
| get.table.ids | Returns the colum names of the differential variability table. |
| get.variability.method | get.variability.method-methods |
| get.variability.method-method | get.variability.method-methods |
| getCellTypesFromLolaDb | getCellTypesFromLolaDb |
| getExecutable | getExecutable-methods |
| getExecutable-method | getExecutable-methods |
| getModuleNumCores | getModuleNumCores-methods |
| getModuleNumCores-method | getModuleNumCores-methods |
| getNamesFromLolaDb | getNamesFromLolaDb |
| getNumNaMeth | getNumNaMeth-methods |
| getNumNaMeth-method | getNumNaMeth-methods |
| getSubCmdStr | getSubCmdStr-methods |
| getSubCmdStr-method | getSubCmdStr-methods |
| getSubCmdTokens | getSubCmdTokens-methods |
| getSubCmdTokens-method | getSubCmdTokens-methods |
| getSubCmdTokens-method | getSubCmdTokens-methods |
| getSubCmdTokens-method | getSubCmdTokens-methods |
| getSubCmdTokens-method | getSubCmdTokens-methods |
| getTargetFromLolaDb | getTargetFromLolaDb |
| greedycut.filter.matrix | greedycut.filter.matrix |
| greedycut.get.statistics | greedycut.get.statistics |
| greedycut.get.submatrix | greedycut.get.submatrix |
-- H --
| has.covariates.ct | has.covariates.ct |
| has.covariates.sva | has.covariates.sva |
| hasCovg | hasCovg-methods |
| hasCovg-method | hasCovg-methods |
-- I --
| includes.sites | includes.sites-methods |
| includes.sites-method | includes.sites-methods |
| infos | RnBeads option values and restrictions |
| initialize-method | Report Class |
| initialize-method | ReportGgPlot Class |
| initialize-method | ReportPlot Class |
| initialize-method | RnBeadClustering Class |
| initialize-method | RnBeadRawSet-class |
| initialize-method | RnBeadSet Class |
| initialize-method | RnBiseqSet Class |
| initialize-method | initialize.ClusterArchitecture |
| initialize-method | initialize.ClusterArchitectureLSF |
| initialize-method | initialize.ClusterArchitectureSGE |
| initialize-method | initialize.ClusterArchitectureSLURM |
| initialize-method | initialize.RnBClusterRun |
| initialize-method | initialize.RnBDiffMeth |
| intensities.by.color | intensities.by.color |
| is.valid | is.valid-methods |
| is.valid-method | is.valid-methods |
| isImputed | isImputed |
| isImputed-method | isImputed |
-- J --
| join.diffMeth | join.diffMeth-methods |
| join.diffMeth-method | join.diffMeth-methods |
-- L --
| limmaP | limmaP |
| load.region.subsegment.annotation | load.region.subsegment.annotation |
| load.rnb.diffmeth | load.rnb.diffmeth |
| load.rnb.set | load.rnb.set |
| loadLolaDbs | loadLolaDbs |
| logger.argument | logger.argument |
| logger.close | Log File Management |
| logger.completed | Log File Management |
| logger.error | Writing text messages to the log file. |
| logger.getfiles | logger.getfiles |
| logger.info | Writing text messages to the log file. |
| logger.isinitialized | logger.isinitialized |
| logger.machine.name | logger.machine.name |
| logger.start | Log File Management |
| logger.status | Writing text messages to the log file. |
| logger.validate.file | logger.validate.file |
| logger.warning | Writing text messages to the log file. |
| lolaBarPlot | lolaBarPlot |
| lolaBoxPlotPerTarget | lolaBoxPlotPerTarget |
| lolaVolcanoPlot | lolaVolcanoPlot |
| lump.hg19 | LUMP Support |
| lump.hg38 | LUMP Support (hg38) |
-- M --
| M | M-methods |
| M-method | M-methods |
| mask.sites.meth | mask.sites.meth-methods |
| mask.sites.meth-method | mask.sites.meth-methods |
| mergeSamples | mergeSamples |
| mergeSamples-method | mergeSamples |
| meth | meth-methods |
| meth-method | meth-methods |
| mval | mval-methods |
| mval-method | mval-methods |
-- N --
| nsites | nsites-methods |
| nsites-method | nsites-methods |
-- O --
| off | off-methods |
| off-method | off-methods |
-- P --
| 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 | pheno-methods |
| pheno-method | pheno-methods |
| prepareSOFTfileForGEO | prepareSOFTfileForGEO |
| previous | RnBeads option values and restrictions |
-- Q --
| qc | qc-methods |
| qc-method | qc-methods |
-- R --
| 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 | regionMapping-methods |
| regionMapping-method | regionMapping-methods |
| regions | regions-methods |
| regions-method | regions-methods |
| reload | reload-methods |
| reload-method | reload-methods |
| remove.regions | remove.regions-methods |
| remove.regions-method | remove.regions-methods |
| remove.samples | remove.samples-methods |
| remove.samples-method | remove.samples-methods |
| remove.sites | remove.sites-methods |
| remove.sites-method | 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.annotation.size | rnb.annotation.size |
| rnb.annotation2data.frame | rnb.annotation2data.frame |
| 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 |
| rnb.color.legends | rnb.color.legends |
| rnb.combine.arrays | Combine array-based datasets |
| rnb.combine.seq | rnb.combine.seq |
| rnb.execute.age.prediction | rnb.execute.age.prediction |
| rnb.execute.batch.qc | rnb.execute.batch.qc |
| rnb.execute.batcheffects | rnb.execute.batcheffects |
| 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.high.dpval.masking | rnb.execute.high.dpval.masking |
| 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.pOOBAH | rnb.execute.pOOBAH |
| 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.getOption | RnBeads Options |
| rnb.infinium.control.targets | rnb.infinium.control.targets |
| rnb.initialize.reports | rnb.initialize.reports |
| 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.nv.heatmap | rnb.plot.nv.heatmap |
| 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.differential | RnBeads Modules in the Analysis Pipeline |
| rnb.run.dj | rnb.run.dj |
| rnb.run.example | rnb.run.example |
| rnb.run.exploratory | RnBeads Modules in the Analysis Pipeline |
| rnb.run.import | RnBeads Modules in the Analysis Pipeline |
| rnb.run.inference | RnBeads Modules in the Analysis Pipeline |
| rnb.run.preprocessing | RnBeads Modules in the Analysis Pipeline |
| rnb.run.qc | RnBeads Modules in the Analysis Pipeline |
| rnb.run.tnt | 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.sample.summary.table-method | 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 |
| 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 |
| RnBClusterRun-class | RnBClusterRun Class |
| RnBDiffMeth-class | RnBDiffMeth Class |
| RnBeadClustering-class | RnBeadClustering Class |
| RnBeadRawSet | RnBeadRawSet-class |
| RnBeadRawSet-class | RnBeadRawSet-class |
| RnBeads | Analysis of genome-scale DNA methylation data with RnBeads |
| RnBeads.data | RnBeads Annotation Tables |
| RnBeadSet | RnBeadSet Class |
| RnBeadSet-class | RnBeadSet Class |
| RnBiseqSet | RnBiseqSet Class |
| RnBiseqSet-class | RnBiseqSet Class |
| RnBSet-class | RnBSet Class |
| rowOneSampleTP | rowOneSampleTP |
| rowPairedTP | rowPairedTP |
| rowWelchP | rowWelchP |
| run | run-methods |
| run-method | run-methods |
| run.cross.validation | run.cross.validation |
-- S --
| sampleCovgApply | sampleCovgApply-methods |
| sampleCovgApply-method | sampleCovgApply-methods |
| sampleMethApply | sampleMethApply-methods |
| sampleMethApply-method | sampleMethApply-methods |
| samples | samples-methods |
| samples-method | samples-methods |
| save.rnb.diffmeth | save.rnb.diffmeth |
| save.rnb.set | save.rnb.set |
| save.tables | save.tables-methods |
| save.tables-method | save.tables-methods |
| set.covariates.ct | set.covariates.ct |
| set.covariates.sva | set.covariates.sva |
| setExecutable | setExecutable-methods |
| setExecutable-method | setExecutable-methods |
| setModuleNumCores | setModuleNumCores-methods |
| setModuleNumCores-method | setModuleNumCores-methods |
| setModuleResourceRequirements | setModuleResourceRequirements-methods |
| setModuleResourceRequirements-method | setModuleResourceRequirements-methods |
| sites | sites-methods |
| sites-method | sites-methods |
| summarize.regions | summarize.regions-methods |
| summarize.regions-method | summarize.regions-methods |
| summarized.regions | summarized.regions-methods |
| summarized.regions-method | summarized.regions-methods |
-- U --
| U | U-methods |
| U-method | U-methods |
| updateMethylationSites | updateMethylationSites-methods |
| updateMethylationSites-method | updateMethylationSites-methods |
| updateRegionSummaries | updateRegionSummaries |
| updateRegionSummaries-method | updateRegionSummaries |
-- misc --
| [-method | Extract parts of BigFfMat |
| [<--method | Replace parts of BigFfMat |