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"exportDMRs2regionFile", "title": "exportDMRs2regionFile", "topics": [ "exportDMRs2regionFile" ] }, { "page": "geno", "title": "geno-methods", "topics": [ "geno", "geno,RnBSet-method" ] }, { "page": "get.adjustment.variables", "title": "get.adjustment.variables", "topics": [ "get.adjustment.variables" ] }, { "page": "get.comparison.grouplabels-RnBDiffMeth-methods", "title": "get.comparison.grouplabels-methods", "topics": [ "get.comparison.grouplabels", "get.comparison.grouplabels,RnBDiffMeth-method" ] }, { "page": "get.comparison.groupsizes-RnBDiffMeth-methods", "title": "get.comparison.groupsizes-methods", "topics": [ "get.comparison.groupsizes", "get.comparison.groupsizes,RnBDiffMeth-method" ] }, { "page": "get.comparison.info", "title": "get.comparison.info", "topics": [ "get.comparison.info" ] }, { "page": "get.comparisons-RnBDiffMeth-methods", "title": "get.comparisons-methods", "topics": [ "get.comparisons", "get.comparisons,RnBDiffMeth-method" ] }, { "page": "get.covariates.ct", "title": "get.covariates.ct", "topics": [ "get.covariates.ct" ] }, { "page": "get.covariates.sva", "title": "get.covariates.sva", "topics": [ "get.covariates.sva" ] }, { "page": "get.covg.thres-RnBDiffMeth-methods", "title": "get.covg.thres-methods", "topics": [ "get.covg.thres", "get.covg.thres,RnBDiffMeth-method" ] }, { "page": "get.cpg.stats", "title": "get.cpg.stats", "topics": [ "get.cpg.stats" ] }, { "page": "get.files", "title": "get.files", "topics": [ "get.files" ] }, { "page": "get.region.types-RnBDiffMeth-methods", "title": "get.region.types-methods", "topics": [ "get.region.types", "get.region.types,RnBDiffMeth-method" ] }, { "page": "get.site.test.method-RnBDiffMeth-methods", "title": "get.site.test.method-methods", "topics": [ "get.site.test.method", "get.site.test.method,RnBDiffMeth-method" ] }, { "page": "get.table-RnBDiffMeth-methods", "title": "get.table-methods", "topics": [ "get.table", "get.table,RnBDiffMeth-method" ] }, { "page": "get.table.ids", "title": "Returns the colum names of the differential variability table.", "topics": [ "get.table.ids" ] }, { "page": "get.variability.method-RnBDiffMeth-methods", "title": "get.variability.method-methods", "topics": [ "get.variability.method", "get.variability.method,RnBDiffMeth-method" ] }, { "page": "getCellTypesFromLolaDb", "title": "getCellTypesFromLolaDb", "topics": [ "getCellTypesFromLolaDb" ] }, { "page": "getExecutable-ClusterArchitecture-methods", "title": "getExecutable-methods", "topics": [ "getExecutable", "getExecutable,ClusterArchitecture,character-method", "getExecutable,ClusterArchitecture-method" ] }, { "page": "getModuleNumCores-RnBClusterRun-methods", "title": "getModuleNumCores-methods", "topics": [ "getModuleNumCores", "getModuleNumCores,RnBClusterRun-method" ] }, { "page": "getNamesFromLolaDb", "title": "getNamesFromLolaDb", "topics": [ "getNamesFromLolaDb" ] }, { "page": "getNumNaMeth-methods", "title": "getNumNaMeth-methods", "topics": [ "getNumNaMeth", "getNumNaMeth,RnBSet-method" ] }, { "page": "getSubCmdStr-ClusterArchitecture-methods", "title": "getSubCmdStr-methods", "topics": [ "getSubCmdStr", "getSubCmdStr,ClusterArchitecture-method" ] }, { "page": "getSubCmdTokens-ClusterArchitecture-methods", "title": "getSubCmdTokens-methods", "topics": [ "getSubCmdTokens", "getSubCmdTokens,ClusterArchitecture-method" ] }, { "page": "getSubCmdTokens-ClusterArchitectureLSF-methods", "title": "getSubCmdTokens-methods", "topics": [ "getSubCmdTokens,ClusterArchitectureLSF-method" ] }, { "page": "getSubCmdTokens-ClusterArchitectureSGE-methods", "title": "getSubCmdTokens-methods", "topics": [ "getSubCmdTokens,ClusterArchitectureSGE-method" ] }, { "page": "getSubCmdTokens-ClusterArchitectureSLURM-methods", "title": "getSubCmdTokens-methods", "topics": [ "getSubCmdTokens,ClusterArchitectureSLURM-method" ] }, { "page": "getTargetFromLolaDb", "title": "getTargetFromLolaDb", "topics": [ "getTargetFromLolaDb" ] }, { "page": "greedycut.filter.matrix", "title": "greedycut.filter.matrix", "topics": [ "greedycut.filter.matrix" ] }, { "page": "greedycut.get.statistics", "title": "greedycut.get.statistics", "topics": [ "greedycut.get.statistics" ] }, { "page": "greedycut.get.submatrix", "title": "greedycut.get.submatrix", "topics": [ "greedycut.get.submatrix" ] }, { "page": "has.covariates.ct", "title": "has.covariates.ct", "topics": [ "has.covariates.ct" ] }, { "page": "has.covariates.sva", "title": "has.covariates.sva", "topics": [ "has.covariates.sva" ] }, { "page": "hasCovg-methods", "title": "hasCovg-methods", "topics": [ "hasCovg", "hasCovg,RnBSet-method" ] }, { "page": "includes.sites-RnBDiffMeth-methods", "title": "includes.sites-methods", "topics": [ "includes.sites", "includes.sites,RnBDiffMeth-method" ] }, { "page": "initialize-ClusterArchitecture-method", "title": "initialize.ClusterArchitecture", "topics": [ "initialize,ClusterArchitecture-method" ] }, { "page": "initialize-ClusterArchitectureLSF-method", "title": "initialize.ClusterArchitectureLSF", "topics": [ "initialize,ClusterArchitectureLSF-method" ] }, { "page": "initialize-ClusterArchitectureSGE-method", "title": "initialize.ClusterArchitectureSGE", "topics": [ "initialize,ClusterArchitectureSGE-method" ] }, { "page": "initialize-ClusterArchitectureSLURM-method", "title": "initialize.ClusterArchitectureSLURM", "topics": [ "initialize,ClusterArchitectureSLURM-method" ] }, { "page": "initialize-RnBClusterRun-method", "title": "initialize.RnBClusterRun", "topics": [ "initialize,RnBClusterRun-method" ] }, { "page": "initialize-RnBDiffMeth-method", "title": "initialize.RnBDiffMeth", "topics": [ "initialize,RnBDiffMeth-method" ] }, { "page": "intensities.by.color", "title": "intensities.by.color", "topics": [ "intensities.by.color" ] }, { "page": "interspecies_probes_v1", "title": "XenoMix interspeciesprobes (v1)", "topics": [ "interspecies_probes_v1" ] }, { "page": "interspecies_probes_v2", "title": "XenoMix interspeciesprobes (v2)", "topics": [ "interspecies_probes_v2" ] }, { "page": "is.valid-RnBDiffMeth-methods", "title": "is.valid-methods", "topics": [ "is.valid", "is.valid,RnBDiffMeth-method" ] }, { "page": "isImputed-RnBSet-method", "title": "isImputed", "topics": [ "isImputed", "isImputed,RnBSet-method" ] }, { "page": "join.diffMeth-methods", "title": "join.diffMeth-methods", "topics": [ "join.diffMeth", "join.diffMeth,RnBDiffMeth,RnBDiffMeth-method" ] }, { "page": "limmaP", "title": "limmaP", "topics": [ "limmaP" ] }, { "page": "load.region.subsegment.annotation", "title": "load.region.subsegment.annotation", "topics": [ "load.region.subsegment.annotation" ] }, { "page": "load.rnb.diffmeth", "title": "load.rnb.diffmeth", "topics": [ "load.rnb.diffmeth" ] }, { "page": "load.rnb.set", "title": "load.rnb.set", "topics": [ "load.rnb.set" ] }, { "page": "loadLolaDbs", "title": "loadLolaDbs", "topics": [ "loadLolaDbs" ] }, { "page": "logger.argument", "title": "logger.argument", "topics": [ "logger.argument" ] }, { "page": "logger.getfiles", "title": "logger.getfiles", "topics": [ "logger.getfiles" ] }, { "page": "logger.isinitialized", "title": "logger.isinitialized", "topics": [ "logger.isinitialized" ] }, { "page": "logger.machine.name", "title": "logger.machine.name", "topics": [ "logger.machine.name" ] }, { "page": "loggerManagement", "title": "Log File Management", "topics": [ "logger.close", "logger.completed", "logger.start" ] }, { "page": "loggerMessages", "title": "Writing text messages to the log file.", "topics": [ "logger.error", "logger.info", "logger.status", "logger.warning" ] }, { "page": "logger.validate.file", "title": "logger.validate.file", "topics": [ "logger.validate.file" ] }, { "page": "lolaBarPlot", "title": "lolaBarPlot", "topics": [ "lolaBarPlot" ] }, { "page": "lolaBoxPlotPerTarget", "title": "lolaBoxPlotPerTarget", "topics": [ "lolaBoxPlotPerTarget" ] }, { "page": "lolaVolcanoPlot", "title": "lolaVolcanoPlot", "topics": [ "lolaVolcanoPlot" ] }, { "page": "lump.hg19", "title": "LUMP Support", "topics": [ "lump.hg19" ] }, { "page": "lump.hg38", "title": "LUMP Support (hg38)", "topics": [ "lump.hg38" ] }, { "page": "M-methods", "title": "M-methods", "topics": [ "M", "M,RnBeadRawSet-method" ] }, { "page": "mask.sites.meth-methods", "title": "mask.sites.meth-methods", "topics": [ "mask.sites.meth", "mask.sites.meth,RnBSet-method" ] }, { "page": "mergeSamples-methods", "title": "mergeSamples", "topics": [ "mergeSamples", "mergeSamples,RnBSet-method" ] }, { "page": "meth-methods", "title": "meth-methods", "topics": [ "meth", "meth,RnBSet-method" ] }, { "page": "mval-methods", "title": "mval-methods", "topics": [ "mval", "mval,RnBSet-method" ] }, { "page": "nsites-methods", "title": "nsites-methods", "topics": [ "nsites", "nsites,RnBSet-method" ] }, { "page": "off", "title": "off-methods", "topics": [ "off", "off,Report-method", "off,ReportGgPlot-method", "off,ReportPlot-method" ] }, { "page": "parallel.getNumWorkers", "title": "parallel.getNumWorkers", "topics": [ "parallel.getNumWorkers" ] }, { "page": "parallel.isEnabled", "title": "parallel.isEnabled", "topics": [ "parallel.isEnabled" ] }, { "page": "parallel.setup", "title": "parallel.setup", "topics": [ "parallel.setup" ] }, { "page": "parallel.teardown", "title": "parallel.teardown", "topics": [ "parallel.teardown" ] }, { "page": "performGoEnrichment.diffMeth", "title": "performGoEnrichment.diffMeth", "topics": [ "performGoEnrichment.diffMeth" ] }, { "page": "performGOenrichment.diffMeth.entrez", "title": "performGOenrichment.diffMeth.entrez", "topics": [ "performGOenrichment.diffMeth.entrez" ] }, { "page": "performGOEnrichment.diffVar", "title": "performGOEnrichment.diffVar", "topics": [ "performGOEnrichment.diffVar" ] }, { "page": "performLolaEnrichment.diffMeth", "title": "performLolaEnrichment.diffMeth", "topics": [ "performLolaEnrichment.diffMeth" ] }, { "page": "performLolaEnrichment.diffVar", "title": "performLolaEnrichment.diffVar", "topics": [ "performLolaEnrichment.diffVar" ] }, { "page": "pheno-methods", "title": "pheno-methods", "topics": [ "pheno", "pheno,RnBSet-method" ] }, { "page": "prepareSOFTfileForGEO", "title": "prepareSOFTfileForGEO", "topics": [ "prepareSOFTfileForGEO" ] }, { "page": "qc-methods", "title": "qc-methods", "topics": [ "qc", "qc,RnBeadSet-method" ] }, { "page": "read.bed.files", "title": "read.bed.files", "topics": [ "read.bed.files" ] }, { "page": "read.data.dir", "title": "read.data.dir", "topics": [ "read.data.dir" ] }, { "page": "read.GS.report", "title": "read.GS.report", "topics": [ "read.GS.report" ] }, { "page": "read.idat.files", "title": "read.idat.files", "topics": [ "read.idat.files" ] }, { "page": "read.idat.files2", "title": "read.idat.files2", "topics": [ "read.idat.files2" ] }, { "page": "read.sample.annotation", "title": "read.sample.annotation", "topics": [ "read.sample.annotation" ] }, { "page": "read.single.bed", "title": "read.single.bed", "topics": [ "read.single.bed" ] }, { "page": "refFreeEWASP", "title": "refFreeEWASP", "topics": [ "refFreeEWASP" ] }, { "page": "regionMapping-methods", "title": "regionMapping-methods", "topics": [ "regionMapping", "regionMapping,RnBSet-method" ] }, { "page": "regions-methods", "title": "regions-methods", "topics": [ "regions", "regions,RnBSet-method" ] }, { "page": "reload-RnBDiffMeth-methods", "title": "reload-methods", "topics": [ "reload", "reload,RnBDiffMeth-method" ] }, { "page": "remove.regions-methods", "title": "remove.regions-methods", "topics": [ "remove.regions", "remove.regions,RnBSet-method" ] }, { "page": "remove.samples-methods", "title": "remove.samples-methods", "topics": [ "remove.samples", "remove.samples,RnBeadRawSet-method", "remove.samples,RnBeadSet-method", "remove.samples,RnBSet-method" ] }, { "page": "remove.sites-methods", "title": "remove.sites-methods", "topics": [ "remove.sites", "remove.sites,RnBeadRawSet-method", "remove.sites,RnBeadSet-method", "remove.sites,RnBSet-method" ] }, { "page": "Report-class", "title": "Report Class", "topics": [ "initialize,Report-method", "Report-class" ] }, { "page": "ReportGgPlot-class", "title": "ReportGgPlot Class", "topics": [ "initialize,ReportGgPlot-method", "ReportGgPlot-class" ] }, { "page": "ReportPlot-class", "title": "ReportPlot Class", "topics": [ "initialize,ReportPlot-method", "ReportPlot-class" ] }, { "page": "rnb.add.figure", "title": "rnb.add.figure", "topics": [ "rnb.add.figure" ] }, { "page": "rnb.add.list", "title": "rnb.add.list", "topics": [ "rnb.add.list" ] }, { "page": "rnb.add.paragraph", "title": "rnb.add.paragraph", "topics": [ "rnb.add.paragraph" ] }, { "page": "rnb.add.reference", "title": "rnb.add.reference", "topics": [ "rnb.add.reference" ] }, { "page": "rnb.add.section", "title": "rnb.add.section", "topics": [ "rnb.add.section" ] }, { "page": "rnb.add.table", "title": "rnb.add.table", "topics": [ "rnb.add.table" ] }, { "page": "rnb.add.tables", "title": "rnb.add.tables", "topics": [ "rnb.add.tables" ] }, { "page": "rnb.annotation.size", "title": "rnb.annotation.size", "topics": [ "rnb.annotation.size" ] }, { "page": "rnb.annotation2data.frame", "title": "rnb.annotation2data.frame", "topics": [ "rnb.annotation2data.frame" ] }, { "page": "rnb.bed.from.segmentation", "title": "rnb.bed.from.segmentation", "topics": [ "rnb.bed.from.segmentation" ] }, { "page": "rnb.beta2mval", "title": "rnb.beta2mval", "topics": [ "rnb.beta2mval" ] }, { "page": "rnb.boxplot.from.segmentation", "title": "rnb.boxplot.from.segmentation", "topics": [ "rnb.boxplot.from.segmentation" ] }, { "page": "rnb.build.index", "title": "rnb.build.index", "topics": [ "rnb.build.index" ] }, { "page": "rnb.call.destructor", "title": "rnb.call.destructor", "topics": [ "rnb.call.destructor" ] }, { "page": "rnb.color.legends", "title": "rnb.color.legends", "topics": [ "rnb.color.legends" ] }, { "page": "rnb.combine.arrays", "title": "Combine array-based datasets", "topics": [ "rnb.combine.arrays" ] }, { "page": "rnb.combine.seq", "title": "rnb.combine.seq", "topics": [ "rnb.combine.seq" ] }, { "page": "rnb.execute.age.prediction", "title": "rnb.execute.age.prediction", "topics": [ "rnb.execute.age.prediction" ] }, { "page": "rnb.execute.batch.qc", "title": "rnb.execute.batch.qc", "topics": [ "rnb.execute.batch.qc" ] }, { "page": "rnb.execute.batcheffects", "title": "rnb.execute.batcheffects", "topics": [ "rnb.execute.batcheffects" ] }, { "page": "rnb.execute.clustering", "title": "rnb.execute.clustering", "topics": [ "rnb.execute.clustering" ] }, { "page": "rnb.execute.clustering.all", "title": "rnb.execute.clustering.all", "topics": [ "rnb.execute.clustering.all" ] }, { "page": "rnb.execute.computeDiffMeth", "title": "rnb.execute.computeDiffMeth", "topics": [ "rnb.execute.computeDiffMeth" ] }, { "page": "rnb.execute.context.removal", "title": "rnb.execute.context.removal", "topics": [ "rnb.execute.context.removal" ] }, { "page": "rnb.execute.cross.reactive.removal", "title": "rnb.execute.cross.reactive.removal", "topics": [ "rnb.execute.cross.reactive.removal" ] }, { "page": "rnb.execute.ct.estimation", "title": "rnb.execute.ct.estimation", "topics": [ "rnb.execute.ct.estimation" ] }, { "page": "rnb.execute.diffVar", "title": "rnb.execute.diffVar", "topics": [ "rnb.execute.diffVar" ] }, { "page": "rnb.execute.dreduction", "title": "rnb.execute.dreduction", "topics": [ "rnb.execute.dreduction" ] }, { "page": "rnb.execute.export.csv", "title": "rnb.execute.export.csv", "topics": [ "rnb.execute.export.csv" ] }, { "page": "rnb.execute.filter.summary", "title": "rnb.execute.filter.summary", "topics": [ "rnb.execute.filter.summary" ] }, { "page": "rnb.execute.gender.prediction", "title": "rnb.execute.gender.prediction", "topics": [ "rnb.execute.gender.prediction" ] }, { "page": "rnb.execute.genomewide", "title": "Genome-wide methylation level", "topics": [ "rnb.execute.genomewide" ] }, { "page": "rnb.execute.greedycut", "title": "rnb.execute.greedycut", "topics": [ "rnb.execute.greedycut" ] }, { "page": "rnb.execute.high.coverage.removal", "title": "rnb.execute.high.coverage.removal", "topics": [ "rnb.execute.high.coverage.removal" ] }, { "page": "rnb.execute.high.dpval.masking", "title": "rnb.execute.high.dpval.masking", "topics": [ "rnb.execute.high.dpval.masking" ] }, { "page": "rnb.execute.import", "title": "rnb.execute.import", "topics": [ "rnb.execute.import" ] }, { "page": "rnb.execute.imputation", "title": "rnb.execute.imputation", "topics": [ "rnb.execute.imputation" ] }, { "page": "rnb.execute.low.coverage.masking", "title": "rnb.execute.low.coverage.masking", "topics": [ "rnb.execute.low.coverage.masking" ] }, { "page": "rnb.execute.lump", "title": "Leukocytes unmethylation for purity", "topics": [ "rnb.execute.lump" ] }, { "page": "rnb.execute.na.removal", "title": "rnb.execute.na.removal", "topics": [ "rnb.execute.na.removal" ] }, { "page": "rnb.execute.normalization", "title": "rnb.execute.normalization", "topics": [ "rnb.execute.normalization" ] }, { "page": "rnb.execute.pOOBAH", "title": "rnb.execute.pOOBAH", "topics": [ "rnb.execute.pOOBAH" ] }, { "page": "rnb.execute.quality", "title": "rnb.execute.quality", "topics": [ "rnb.execute.quality" ] }, { "page": "rnb.execute.segmentation", "title": "rnb.execute.segmentation", "topics": [ "rnb.execute.segmentation" ] }, { "page": "rnb.execute.sex.prediction", "title": "rnb.execute.sex.prediction", "topics": [ "rnb.execute.sex.prediction" ] }, { "page": "rnb.execute.sex.removal", "title": "rnb.execute.sex.removal", "topics": [ "rnb.execute.sex.removal" ] }, { "page": "rnb.execute.snp.removal", "title": "rnb.execute.snp.removal", "topics": [ "rnb.execute.snp.removal" ] }, { "page": "rnb.execute.sva", "title": "rnb.execute.sva", "topics": [ "rnb.execute.sva" ] }, { "page": "rnb.execute.tnt", "title": "rnb.execute.tnt", "topics": [ "rnb.execute.tnt" ] }, { "page": "rnb.execute.training", "title": "rnb.execute.training", "topics": [ "rnb.execute.training" 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