Files in RnBeads

RnBeads

R/CNV.R R/plottingUtils.R R/options.R R/qualityControl.R R/bigFf.R R/differentialVariability.R R/subSegments.R R/annotations.R R/differentialMethylation.R R/genomewide.R R/RnBiseqSet-class.R R/main.R R/batch.R R/sva.R R/profiles.R R/RnBSet-class.R R/dataImport.R R/utilities.R R/agePrediction.R R/Report-methods.R R/readGEO.R R/enmix.R R/cellTypeAdjustment.R R/enrichment.R R/lolaUtils.R R/parallelProcessing.R R/exportGEO.R R/RnBeadSet-class.R R/clusterArchitecture.R R/ReportPlot-methods.R R/clustering.R R/logger.R R/immune.R R/controlPlotsBiSeq.R R/dataExport.R R/clusterArchitectureSLURM.R R/filteringSummary.R R/greedycut.R R/controlPlots.R R/segmentation.R R/Report-class.R R/normalization.R R/regionDescription.R R/RnBDiffMeth-class.R R/ReportPlot-class.R R/computeCluster.R R/loading.R R/clusterArchitectureSGE.R R/bmiq.R R/filtering.R R/sex.R R/regionProfiles.R R/batch.quality.R R/RnBeads-package.R R/combining.R R/RnBeadRawSet-class.R R/wbcInference.R inst/doc/RnBeads_Annotations.pdf inst/doc/RnBeads.R inst/doc/RnBeads_Annotations.R inst/doc/RnBeads.pdf inst/extdata/RnBeadsDJ/app.R inst/extdata/RnBeadsDJ/README.md inst/extdata/Rscript/rscript_wrapup.R inst/extdata/Rscript/rscript_differential_chunk.R inst/extdata/Rscript/rscript_inference.R inst/extdata/Rscript/rscript_qc.R inst/extdata/Rscript/rscript_import.R inst/extdata/Rscript/rscript_preprocessing.R inst/extdata/Rscript/rscript_differential.R inst/extdata/Rscript/rscript_exploratory.R inst/extdata/Rscript/rscript_differential_wrapup.R inst/extdata/Rscript/rscript_tnt.R inst/unitTests/test_others.R inst/unitTests/test_report_3.R inst/unitTests/dataset_generator.R inst/unitTests/test_logger.R inst/unitTests/test_differential.R inst/unitTests/test_report_2.R inst/unitTests/test_report_1.R tests/runTests.R vignettes/figures/mds_sampleGroup.pdf vignettes/figures/snp_heatmap.pdf vignettes/figures/deviationPlot_probeType.pdf vignettes/figures/rnbeads_workflow.pdf vignettes/figures/genomic_covg_plot.pdf vignettes/figures/lola_box.pdf vignettes/figures/increases_gender.pdf vignettes/figures/locusProfile_hoxd3.pdf vignettes/figures/control_boxplot_bad_conversion.pdf vignettes/figures/lola_bar.pdf vignettes/figures/promoter_heatmap.pdf vignettes/figures/sva_adj_pval_qqplot.pdf vignettes/figures/dreduction_custom.pdf vignettes/figures/control_barplot_bad_conversion.pdf vignettes/figures/beta_density.pdf vignettes/figures/segmentation.pdf man/loggerMessages.Rd man/rnb.execute.batcheffects.Rd man/rnb.run.analysis.Rd man/read.sample.annotation.Rd man/rnb.plot.locus.profile.Rd man/read.bed.files.Rd man/greedycut.get.statistics.Rd man/assembly-methods.Rd man/rnb.plot.region.profile.density.Rd man/get.covg.thres-RnBDiffMeth-methods.Rd man/get.comparison.info.Rd man/sampleCovgApply-methods.Rd man/loadLolaDbs.Rd man/updateMethylationSites-methods.Rd man/initialize-ClusterArchitectureSLURM-method.Rd man/rnb.build.index.Rd man/rnb.plot.biseq.coverage.hist.Rd man/rnb.export.annotation.Rd man/rnb.find.relative.site.coord.Rd man/read.GS.report.Rd man/rnb.get.chromosomes.Rd man/samples-methods.Rd man/greedycut.get.submatrix.Rd man/rnb.initialize.reports.Rd man/performLolaEnrichment.diffMeth.Rd man/rnb.add.reference.Rd man/rnb.execute.snp.removal.Rd man/get.cpg.stats.Rd man/rnb.execute.batch.qc.Rd man/M-methods.Rd man/rnb.combine.seq.Rd man/setExecutable-ClusterArchitecture-methods.Rd man/rnb.get.assemblies.Rd man/rnb.sample.summary.table.Rd man/auto.select.rank.cut.Rd man/mergeSamples-methods.Rd man/remove.regions-methods.Rd man/get.comparison.groupsizes-RnBDiffMeth-methods.Rd man/getSubCmdStr-ClusterArchitecture-methods.Rd man/RnBSet-class.Rd man/parallel.isEnabled.Rd man/rnb.plot.biseq.coverage.Rd man/getNamesFromLolaDb.Rd man/U-methods.Rd man/densRanks.Rd man/rnb.get.mapping.Rd man/run-RnBClusterRun-methods.Rd man/rnb.execute.age.prediction.Rd man/estimateProportionsCP.Rd man/get.table.ids.Rd man/parallel.getNumWorkers.Rd man/off-methods.Rd man/getTargetFromLolaDb.Rd man/rnb.execute.training.Rd man/destroy-RnBDiffMeth-methods.Rd man/rnb.RnBSet.to.bed.Rd man/rnb.add.figure.Rd man/apply.iEVORA.Rd man/rnb.infinium.control.targets.Rd man/get.site.test.method-RnBDiffMeth-methods.Rd man/rnb.execute.genomewide.Rd man/rnb.execute.import.Rd man/data.frame2GRanges.Rd man/rnb.section.diffVar.region.Rd man/rnb.message.plot.Rd man/rnb.show.report.Rd man/rnb.set.annotation.and.cpg.stats.Rd man/limmaP.Rd man/getNumNaMeth-methods.Rd man/meth-methods.Rd man/RnBeads.data.Rd man/read.single.bed.Rd man/RnBiseqSet-class.Rd man/mask.sites.meth-methods.Rd man/hasCovg-methods.Rd man/regions-methods.Rd man/load.rnb.diffmeth.Rd man/rnb.execute.clustering.all.Rd man/rnb.sample.groups.Rd man/rnb.step.cnv.Rd man/rnb.export.to.ewasher.Rd man/lolaBoxPlotPerTarget.Rd man/rnb.run.dj.Rd man/ClusterArchitectureSGE-class.Rd man/get.files.Rd man/rnb.execute.na.removal.Rd man/prepareSOFTfileForGEO.Rd man/rnb.color.legends.Rd man/downloadLolaDbs.Rd man/rnb.get.annotation.Rd man/addDiffMethTable-RnBDiffMeth-methods.Rd man/rowOneSampleTP.Rd man/rnb.plot.sentrix.distribution.Rd man/rnb.step.betadistribution.Rd man/RnBClusterRun-class.Rd man/rnb.execute.high.coverage.removal.Rd man/cols.to.rank.Rd man/load.rnb.set.Rd man/rnb.add.list.Rd man/get.covariates.sva.Rd man/rnb.beta2mval.Rd man/rnb.plot.sentrix.distributions.Rd man/pheno-methods.Rd man/ClusterArchitectureSLURM-class.Rd man/getModuleNumCores-RnBClusterRun-methods.Rd man/rnb.execute.variability.removal.Rd man/performLolaEnrichment.diffVar.Rd man/rnb.add.tables.Rd man/rnb.plot.pheno.categories.Rd man/rnb.execute.filter.summary.Rd man/load.region.subsegment.annotation.Rd man/rnb.plot.beta.comparison.Rd man/rnb.plot.negative.boxplot.Rd man/rnb.combine.arrays.Rd man/setModuleNumCores-RnBClusterRun-methods.Rd man/rnb.sample.replicates.Rd man/get.comparisons-RnBDiffMeth-methods.Rd man/createReport.Rd man/remove.sites-methods.Rd man/mval-methods.Rd man/rowPairedTP.Rd man/sub-BigFfMat-ANY-ANY-ANY-method.Rd man/read.idat.files2.Rd man/has.covariates.ct.Rd man/rnb.add.paragraph.Rd man/performGoEnrichment.diffMeth.Rd man/rnb.performance.profile.Rd man/logger.machine.name.Rd man/updateRegionSummaries.Rd man/rnb.remove.annotation.Rd man/rnb.RnBSet.to.GRangesList.Rd man/set.covariates.ct.Rd man/rnb.get.directory.Rd man/rnb.execute.dreduction.Rd man/addRegionSubsegments.Rd man/remove.samples-methods.Rd man/nsites-methods.Rd man/get.region.types-RnBDiffMeth-methods.Rd man/rnb.plot.ct.heatmap.Rd man/refFreeEWASP.Rd man/createReportPlot.Rd man/rnb.load.sitelist.Rd man/computeDiffTab.region.Rd man/sampleMethApply-methods.Rd man/rnb.execute.computeDiffMeth.Rd man/ReportGgPlot-class.Rd man/rnb.bed.from.segmentation.Rd man/getCellTypesFromLolaDb.Rd man/get.table-RnBDiffMeth-methods.Rd man/rnb.execute.imputation.Rd man/performGOenrichment.diffMeth.entrez.Rd man/rnb.execute.diffVar.Rd man/as.RnBeadRawSet.Rd man/lump.hg38.Rd man/logger.argument.Rd man/create.hex.summary.plot.Rd man/create.scatter.dens.points.Rd man/rnb.plot.snp.boxplot.Rd man/logger.getfiles.Rd man/logger.isinitialized.Rd man/set.covariates.sva.Rd man/rnb.execute.cross.reactive.removal.Rd man/getExecutable-ClusterArchitecture-methods.Rd man/rnb.boxplot.from.segmentation.Rd man/rnb.execute.ct.estimation.Rd man/rnb.run.xml.Rd man/accepted.Rd man/get.variability.method-RnBDiffMeth-methods.Rd man/rnb.plot.biseq.coverage.violin.Rd man/rnb.options.Rd man/join.diffMeth-methods.Rd man/dim-BigFfMat-method.Rd man/regionMapping-methods.Rd man/getSubCmdTokens-ClusterArchitectureSGE-methods.Rd man/rnb.execute.quality.Rd man/ClusterArchitecture-class.Rd man/initialize-RnBClusterRun-method.Rd man/includes.sites-RnBDiffMeth-methods.Rd man/initialize-RnBDiffMeth-method.Rd man/rnb.export.to.trackhub.Rd man/RnBeadClustering-class.Rd man/rnb.load.annotation.Rd man/destroy-methods.Rd man/lolaVolcanoPlot.Rd man/RnBeadSet-class.Rd man/combine-methods.Rd man/rnb.get.reference.Rd man/rnb.plot.marker.fstat.Rd man/rnb.set.annotation.Rd man/rnb.export.all.annotation.Rd man/rnb.add.section.Rd man/rnb.plot.region.site.density.Rd man/rnb.plot.control.boxplot.Rd man/exportDMRs2regionFile.Rd man/BMIQ.Rd man/rnb.execute.greedycut.Rd man/rnb.save.annotation.Rd man/RnBeadRawSet-class.Rd man/rnb.execute.low.coverage.masking.Rd man/deviation.plot.beta.Rd man/setModuleResourceRequirements-RnBClusterRun-methods.Rd man/rnb.xml2options.Rd man/read.idat.files.Rd man/rnb.plot.control.barplot.Rd man/qc-methods.Rd man/get.adjustment.variables.Rd man/rnb.load.annotation.from.db.Rd man/getSubCmdTokens-ClusterArchitecture-methods.Rd man/dpval-methods.Rd man/lump.hg19.Rd man/rnb.options2xml.Rd man/lolaBarPlot.Rd man/parallel.setup.Rd man/rnb.plot.num.sites.covg.Rd man/performGOEnrichment.diffVar.Rd man/rnb.execute.sex.removal.Rd man/rnb.execute.gender.prediction.Rd man/combineTestPvalsMeth.Rd man/loggerManagement.Rd man/createReportGgPlot.Rd man/diffVar.Rd man/rnb.add.table.Rd man/parallel.teardown.Rd man/coercion-methods.Rd man/rnb.run.example.Rd man/sites-methods.Rd man/rnb.execute.export.csv.Rd man/save.tables-RnBDiffMeth-methods.Rd man/save.rnb.set.Rd man/isImputed-RnBSet-method.Rd man/rnb.plot.region.profiles.Rd man/addPheno-RnBSet-methods.Rd man/RnBeads.Rd man/annotation-methods.Rd man/subset-BigFfMat-ANY-ANY-ANY-method.Rd man/covg-methods.Rd man/rnb.RnBSet.to.bedGraph.Rd man/rnb.mval2beta.Rd man/run.cross.validation.Rd man/rnb.runs.Rd man/get.comparison.grouplabels-RnBDiffMeth-methods.Rd man/rowWelchP.Rd man/save.rnb.diffmeth.Rd man/RnBDiffMeth-class.Rd man/rnb.get.reliability.matrix.Rd man/rnb.execute.segmentation.Rd man/rnb.plot.betadistribution.sampleGroups.Rd man/get.covariates.ct.Rd man/rnb.plot.coverage.thresholds.Rd man/is.valid-RnBDiffMeth-methods.Rd man/has.covariates.sva.Rd man/rnb.execute.normalization.Rd man/rnb.execute.sva.Rd man/rnb.plot.dreduction.Rd man/rnb.execute.lump.Rd man/getSubCmdTokens-ClusterArchitectureSLURM-methods.Rd man/rnb.plot.snp.heatmap.Rd man/rnb.execute.context.removal.Rd man/reload-RnBDiffMeth-methods.Rd man/computeDiffTab.site.Rd man/initialize-ClusterArchitectureSGE-method.Rd man/combine.diffMeth.objs.Rd man/rnb.execute.clustering.Rd man/intensities.by.color.Rd man/rnb.region.types.for.analysis.Rd man/read.data.dir.Rd man/rnb.annotation.size.Rd man/Report-class.Rd man/rnb.execute.tnt.Rd man/rnb.read.geo.Rd man/rnb.execute.sex.prediction.Rd man/logger.validate.file.Rd man/rnb.annotation2data.frame.Rd man/rnb.plot.betadistribution.probeCategories.Rd man/ReportPlot-class.Rd man/create.densityScatter.Rd man/summarize.regions-methods.Rd man/rnb.write.table.Rd man/rnb.plot.snp.barplot.Rd man/greedycut.filter.matrix.Rd man/rnb.is.option.Rd man/summarized.regions-methods.Rd man/initialize-ClusterArchitecture-method.Rd man/rnb.region.types.Rd man/rnb.call.destructor.Rd