A B C D E G H I J L M N O P Q R S T U W
RnBeads-package | Analysis of genome-scale DNA methylation data with RnBeads |
accepted | RnBeads option values and restrictions |
add.age.histogram | add.age.histogram |
add.agecomparison.plot | add.agecomparison.plot |
add.combination.plot | add.combination.plot |
add.error.plot | add.error.plot |
add.quantile.plot | add.quantile.plot |
addDiffMethTable | addDiffMethTable-methods |
addDiffMethTable-method | addDiffMethTable-methods |
addPheno | addPheno |
addPheno-method | addPheno |
addRegionSubsegments | addRegionSubsegments |
age.anti.transformation | age.anti.transformation |
age.transformation | age.transformation |
agePredictor | agePredictor |
agePredictor450 | agePredictor450 |
agePredictorRRBS | agePredictorRRBS |
annotation | annotation-methods |
annotation-method | annotation-methods |
as.RnBeadRawSet | as("MethyLumiSet", "RnBeadRawSet") |
assembly | assembly-methods |
assembly-method | assembly-methods |
auto.select.rank.cut | auto.select.rank.cut |
BMIQ | BMIQ |
ClusterArchitecture-class | ClusterArchitecture Class |
ClusterArchitectureSGE-class | ClusterArchitectureSGE Class |
coercion-methods | as("RnBeadSet", "MethyLumiSet") |
combine-method | combine-methods |
combine.diffMeth.objs | combine.diffMeth.objs |
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 |
createPredictor | createPredictor |
createReport | createReport |
createReportGgPlot | createReportGgPlot |
createReportPlot | createReportPlot |
current | RnBeads option values and restrictions |
cv.array | cv.array |
cv.biseq | cv.biseq |
data.frame2GRanges | data.frame2GRanges |
densRanks | densRanks |
destroy | destroy-methods |
destroy-method | destroy-methods |
destroy-method | destroy-methods |
deviation.plot.beta | deviation.plot.beta |
dpval | dpval-methods |
dpval-method | dpval-methods |
estimateProportionsCP | estimateProportionsCP |
exportDMRs2regionFile | exportDMRs2regionFile |
general.cv | general.cv |
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 |
getExecutable | getExecutable-methods |
getExecutable-method | getExecutable-methods |
getModuleNumCores | getModuleNumCores-methods |
getModuleNumCores-method | getModuleNumCores-methods |
getSubCmdStr | getSubCmdStr-methods |
getSubCmdStr-method | getSubCmdStr-methods |
getSubCmdTokens | getSubCmdTokens-methods |
getSubCmdTokens-method | getSubCmdTokens-methods |
getSubCmdTokens-method | getSubCmdTokens-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 | hasCovg-methods |
hasCovg-method | hasCovg-methods |
imputeRRBS | imputeRRBS |
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.ClusterArchitectureSGE |
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 |
join.diffMeth | join.diffMeth-methods |
join.diffMeth-method | join.diffMeth-methods |
limmaP | limmaP |
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.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. |
M | M-methods |
M-method | M-methods |
mergeSamples | mergeSamples |
mergeSamples-method | mergeSamples |
meth | meth-methods |
meth-method | meth-methods |
mval | mval-methods |
mval-method | mval-methods |
nsites | nsites-methods |
nsites-method | nsites-methods |
off | off-methods |
off-method | off-methods |
parallel.getNumWorkers | parallel.getNumWorkers |
parallel.isEnabled | parallel.isEnabled |
parallel.setup | parallel.setup |
parallel.teardown | parallel.teardown |
performEnrichment.diffMeth | performEnrichment.diffMeth |
performGOenrichment.diffMeth.entrez | performGOenrichment.diffMeth.entrez |
pheno | pheno-methods |
pheno-method | pheno-methods |
previous | RnBeads option values and restrictions |
qc | qc-methods |
qc-method | qc-methods |
read.bed.files | read.bed.files |
read.data.dir | read.data.dir |
read.geo | read.geo |
read.geo.parse.characteristics_ch1 | read.geo.parse.characteristics_ch1 |
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.beta2mval | rnb.beta2mval |
rnb.build.index | rnb.build.index |
rnb.call.destructor | rnb.call.destructor |
rnb.color.legends | rnb.color.legends |
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.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.greedycut | rnb.execute.greedycut |
rnb.execute.high.coverage.removal | rnb.execute.high.coverage.removal |
rnb.execute.import | rnb.execute.import |
rnb.execute.low.coverage.masking | rnb.execute.low.coverage.masking |
rnb.execute.na.removal | rnb.execute.na.removal |
rnb.execute.normalization | rnb.execute.normalization |
rnb.execute.quality | rnb.execute.quality |
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.age.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.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.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 | rnb.RnBSet.to.bed |
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.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.ageprediction | rnb.section.ageprediction |
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.ageprediction | rnb.step.ageprediction |
rnb.step.betadistribution | rnb.step.betadistribution |
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 |
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 |
simpleGlmnet | simpleGlmnet |
simpleGlmnetEvaluate | simpleGlmnetEvaluate |
simpleGlmnetRRBS | simpleGlmnetRRBS |
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 |
trainPredictor | trainPredictor |
U | U-methods |
U-method | U-methods |
updateRegionSummaries | updateRegionSummaries |
updateRegionSummaries-method | updateRegionSummaries |
writePredictorToCsv | writePredictorToCsv |