lumi
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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222
Source code
51
Man pages
88
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lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
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API

API for lumi
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Global functions
.estimate.quantile.reference Source code
.initialGammaEstimation Source code
.quantileNormalization.reference Source code
IlluminaID2nuID Man page
LumiBatch Man page
LumiBatch-class Man page
MAplot Man page
MAplot,ExpressionSet-method Man page
MAplot-methods Man page
MAplot.ExpressionSet Man page
[,LumiBatch,ANY,ANY,ANY-method Man page
[,LumiBatch-method Man page
`IlluminaID2nuID` Source code
`addControlData2lumi` Source code
`addNuID2lumi` Source code
`addNuId2lumi` Source code
`detectOutlier` Source code
`detectionCall` Source code
`estimateLumiCV` Source code
`getChipInfo` Source code
`getControlData` Source code
`getControlProbe` Source code
`getControlType` Source code
`getNuIDMappingInfo` Source code
`id2seq` Source code
`inverseVST` Source code
`is.nuID` Source code
`lumiN` Source code
`lumiQ` Source code
`lumiR` Source code
`lumiT` Source code
`monoSmu` Source code
`monoSpline` Source code
`nuID2EntrezID` Source code
`nuID2IlluminaID` Source code
`nuID2RefSeqID` Source code
`plotControlData` Source code
`plotHousekeepingGene` Source code
`plotSampleRelation` Source code
`plotStringencyGene` Source code
`plotVST` Source code
`produceGEOPlatformFile` Source code
`produceGEOSampleInfoTemplate` Source code
`produceGEOSubmissionFile` Source code
`produceMethylationGEOSubmissionFile` Source code
`rankinvariant` Source code
`rsn` Source code
`seq2id` Source code
`ssn` Source code
`vst` Source code
addAnnotationInfo Man page Source code
addControlData2lumi Man page
addControlData2methyLumiM Man page Source code
addNuID2lumi Man page
addNuId2lumi Man page
adjColorBias.quantile Man page Source code
adjColorBias.ssn Man page Source code
asBigMatrix Man page
asBigMatrix,ExpressionSet-method Man page
asBigMatrix-methods Man page
beadNum Man page
beadNum,ExpressionSet-method Man page
beadNum<- Man page
beadNum<-,ExpressionSet,ANY-method Man page
beadNum<-,ExpressionSet-method Man page
beta2m Man page Source code
bgAdjust Man page Source code
bgAdjustMethylation Man page Source code
boxplot,ExpressionSet-method Man page
boxplot,MethyLumiM-method Man page
boxplot-methods Man page
boxplot.ExpressionSet Man page
boxplotColorBias Man page Source code
class:LumiBatch Man page
colorBiasSummary Man page Source code
combine,ExpressionSet,LumiBatch-method Man page
combine,LumiBatch,ExpressionSet-method Man page
combine,LumiBatch,LumiBatch-method Man page
controlData Man page
controlData,LumiBatch-method Man page
controlData<- Man page
controlData<-,LumiBatch,ANY-method Man page
controlData<-,LumiBatch-method Man page
density,ExpressionSet-method Man page
density-methods Man page
density.ExpressionSet Man page
detectOutlier Man page
detection Man page
detection,ExpressionSet-method Man page
detection<- Man page
detection<-,ExpressionSet,ANY-method Man page
detection<-,ExpressionSet-method Man page
detectionCall Man page
estimateBeta Man page Source code
estimateIntensity Man page Source code
estimateLumiCV Man page
estimateM Man page Source code
estimateMethylationBG Man page Source code
example.lumi Man page
example.lumiMethy Man page
example.methyTitration Man page
gammaFitEM Man page Source code
getChipInfo Man page
getChrInfo Man page Source code
getControlData Man page
getControlProbe Man page
getControlType Man page
getHistory Man page
getHistory,LumiBatch-method Man page
getNuIDMappingInfo Man page
hist,ExpressionSet-method Man page
hist-methods Man page
hist.ExpressionSet Man page
id2seq Man page
importMethyIDAT Man page Source code
initialize,LumiBatch-method Man page
inverseVST Man page
is.nuID Man page
lumi Man page
lumi-package Man page
lumiB Man page Source code
lumiExpresso Man page
lumiMethyB Man page Source code
lumiMethyC Man page Source code
lumiMethyN Man page Source code
lumiMethyR Man page Source code
lumiMethyStatus Man page Source code
lumiN Man page
lumiQ Man page
lumiR Man page
lumiR.batch Man page Source code
lumiT Man page
m2beta Man page Source code
methylationCall Man page Source code
monoSmu Man page
monoSpline Man page
normalizeMethylation.quantile Man page Source code
normalizeMethylation.ssn Man page Source code
nuID2EntrezID Man page
nuID2IlluminaID Man page
nuID2RefSeqID Man page
nuID2probeID Man page Source code
nuID2targetID Man page Source code
pairs,ExpressionSet-method Man page
pairs-methods Man page
pairs.ExpressionSet Man page
plot,ExpressionSet,missing-method Man page
plot,ExpressionSet-method Man page
plot-methods Man page
plot.ExpressionSet Man page
plotCDF Man page Source code
plotCDF,ExpressionSet-method Man page
plotCDF.ExpressionSet Man page
plotColorBias1D Man page Source code
plotColorBias2D Man page Source code
plotControlData Man page
plotDensity Man page Source code
plotDensity.ExpressionSet Man page
plotGammaFit Man page Source code
plotHousekeepingGene Man page
plotSampleRelation Man page
plotStringencyGene Man page
plotVST Man page
probeID2nuID Man page Source code
produceGEOPlatformFile Man page
produceGEOSampleInfoTemplate Man page
produceGEOSubmissionFile Man page
produceMethylationGEOSubmissionFile Man page Source code
rankinvariant Man page
rsn Man page
sampleNames<-,LumiBatch,ANY-method Man page
se.exprs Man page
se.exprs,ExpressionSet-method Man page
se.exprs<- Man page
se.exprs<-,ExpressionSet,ANY-method Man page
se.exprs<-,ExpressionSet-method Man page
seq2id Man page
show,LumiBatch-method Man page
smoothQuantileNormalization Man page Source code
ssn Man page
summary,LumiBatch-method Man page
targetID2nuID Man page Source code
valid_controlData Source code
vst Man page
lumi documentation built on Nov. 8, 2020, 5:27 p.m.

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