lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

AuthorPan Du, Richard Bourgon, Gang Feng, Simon Lin
Date of publicationNone
MaintainerPan Du <dupan.mail@gmail.com>, Lei Huang <lhuang@bsd.uchicago.edu>, Gang Feng <g-feng@northwestern.edu>
LicenseLGPL (>= 2)
Version2.26.4

View on Bioconductor

Man pages

addAnnotationInfo: Add probe color channel and basic annotation information...

addControlData2lumi: Add the control probe data into the controlData slot of...

addControlData2methyLumiM: Add methylation control data to a MethyLumiM object

addNuID2lumi: Add the nuID information to the LumiBatch object

adjColorBias.quantile: Color bias adjustment of Illumina Infinium methylaton...

adjColorBias.ssn: Color bias adjustment of Illumina Infinium methylaton...

asBigMatrix-methods: convert the data matrix in the assayData of a ExpressionSet...

beta2m: Convert methylation Beta-value to M-value

bgAdjust: Background adjustment for Illumina data

bgAdjustMethylation: Estimate and adjust the background levels of Illumina...

boxplotColorBias: Plot the Illumina Infinium methylation color bias in terms of...

boxplot-methods: boxplot of a ExpressionSet object

boxplot-MethyLumiM-methods: boxplot of a MethyLumiM object

colorBiasSummary: A summary of colorBias information

density-methods: Density plot of a ExpressionSet object

detectionCall: Estimate the detectable probe ratio

detectOutlier: Detect the outlier sample (or gene)

estimateBeta: Estimate methylation Beta-value matrix

estimateIntensity: Estimate intensity of Illumina methylation data

estimateLumiCV: Estimate the coefficient of variance matrix of LumiBatch...

estimateM: Estimate methylation M-value matrix

estimateMethylationBG: Estimate the background levels of Illumina Infinium...

example.lumi: Example Illumina Expression data in LumiBatch class

example.lumiMethy: Example Illumina Infinium Methylation data in MethyLumiM...

example.methyTitration: Example Illumina Infinium Methylation titration data in...

gammaFitEM: Estimate the methylation status by fitting a Gamma mixture...

getChipInfo: Get Illumina Chip Information based on probe identifiers

getChrInfo: get the chromosome location information of methylation probes

getControlData: Get control probe information

getControlProbe: Get the control probe Ids

getControlType: Get the types of the control probes

getNuIDMappingInfo: get the mapping information from nuID to RefSeq ID

hist-methods: Density plot of a ExpressionSet object

id2seq: Transfer a nuID as a nucleotide sequence

IlluminaID2nuID: Matching Illumina IDs to nuID based on Illumina ID mapping...

importMethyIDAT: Import Illumina methylation .idat files as an MethyLumiM...

inverseVST: Inverse VST transform

is.nuID: nuID self-identification

lumiB: Background correction of Illumina Expression data

LumiBatch-class: Class LumiBatch: contain and describe Illumina microarray...

lumiExpresso: From raw Illumina probe intensities to expression values

lumiMethyB: Adjust background level of Illumina Infinium methylation data

lumiMethyC: Color bias adjust of Illumina Infinium methylation data

lumiMethyN: Normalize the Illumina Infinium methylation data

lumiMethyR: Reading Illumina methylation microarray data

lumiMethyStatus: Estimate the methylation status of individual methylation...

lumiN: Between chip normalization of a LumiBatch object

lumi.package: A package for preprocessing Illumina microarray data

lumiQ: Quality control evaluation of the LumiBatch object

lumiR: Read in Illumina expression data

lumiR.batch: Read BeadStudio output files in batch

lumiT: Transfer the Illumina data to stabilize the variance

m2beta: Convert methylation M-value to Beta-value

MAplot-methods: MAplot of a ExpressionSet object

methylationCall: Estimated methylation call

monoSmu: Monotonic smooth method

monoSpline: Fitting a curve with monotonic spline

normalizeMethylation.quantile: Quantile normalization of Illumina Infinium methylation data...

normalizeMethylation.ssn: Shift and scaling normalization of Illumina Infinium...

nuID2EntrezID: Map nuID to Entrez ID

nuID2IlluminaID: Matching nuIDs to Illumina IDs based on Illumina ID mapping...

nuID2probeID: Mapping nuID into Illumina ProbeID

nuID2RefSeqID: Map nuID to RefSeq ID

nuID2targetID: Mapping nuID into Illumina TargetID

pairs-methods: Pair plot of an ExpressionSet object

plotCDF: plot the cumulative distribution function of a ExpressionSet...

plotColorBias1D: Plot the color bias density plot of Illumina Infinium...

plotColorBias2D: Plot the color bias of Illumina Infinium Methylation data in...

plotControlData: Plot the mean expression (with standard deviation bar) of...

plotDensity: plot the density distribution

plotGammaFit: plot the fitting results of 'gammaFitEM'

plotHousekeepingGene: Plot the housekeeping gene expression profile

plot-methods: Plot of a ExpressionSet object

plotSampleRelation: visualize the sample relations

plotStringencyGene: plot the Stringency related control probe profiles

plotVST: plot the VST (Variance Stabilizing Transform) function

probeID2nuID: Mapping Illumina ProbeID as nuID

produceGEOPlatformFile: Produce GEO Platform Submission File in SOFT format

produceGEOSampleInfoTemplate: Produce the template of GEO sample information

produceGEOSubmissionFile: Produce GEO Sample Submission File in SOFT format

produceMethylationGEOSubmissionFile: Produce GEO Sample Submission File of Illumina methylation...

rankinvariant: Rank Invariant Normalization

rsn: Robust Spline Normalization between chips

seq2id: Transfer a nucleotide sequence as a nuID

smoothQuantileNormalization: Smooth quantile normalization

ssn: Simple Scaling Normalization

targetID2nuID: Mapping Illumina TargetID (GeneID) into nuID

vst: Variance Stabilizing Transformation

Functions

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

Files

lumi/DESCRIPTION
lumi/NAMESPACE
lumi/NEWS
lumi/R
lumi/R/AllGenerics.R lumi/R/IlluminaID2nuID.R lumi/R/LumiBatch-class.R lumi/R/addControlData2lumi.R lumi/R/addNuID2lumi.R lumi/R/bgAdjust.R lumi/R/detectOutlier.R lumi/R/detectionCall.R lumi/R/estimateLumiCV.R lumi/R/getChipInfo.R lumi/R/getControlData.R lumi/R/getControlProbe.R lumi/R/getControlType.R lumi/R/getNuIDMappingInfo.R lumi/R/id2seq.R lumi/R/inverseVST.R lumi/R/is.nuID.R lumi/R/lumiB.R lumi/R/lumiExpresso.R lumi/R/lumiN.R lumi/R/lumiQ.R lumi/R/lumiR.R lumi/R/lumiR.batch.R lumi/R/lumiT.R lumi/R/methylation_preprocessing.R lumi/R/monoSmu.R lumi/R/monoSpline.R lumi/R/nuID2EntrezID.R lumi/R/nuID2IlluminaID.R lumi/R/nuID2RefSeqID.R lumi/R/nuIDMapping.R lumi/R/plotCDF.R lumi/R/plotControlData.R lumi/R/plotHousekeepingGene.R lumi/R/plotSampleRelation.R lumi/R/plotStringencyGene.R lumi/R/plotVST.R lumi/R/produceGEOPlatformFile.R lumi/R/produceGEOSampleInfoTemplate.R lumi/R/produceGEOSubmissionFile.R lumi/R/produceMethylationGEOSubmissionFile.R lumi/R/rankinvariant.R lumi/R/rsn.R lumi/R/seq2id.R lumi/R/ssn.R lumi/R/vst.R lumi/R/zzz.R
lumi/data
lumi/data/datalist
lumi/data/example.lumi.rda
lumi/data/example.lumiMethy.rda
lumi/data/example.methyTitration.rda
lumi/inst
lumi/inst/CITATION
lumi/man
lumi/man/IlluminaID2nuID.Rd lumi/man/LumiBatch-class.Rd lumi/man/MAplot-methods.Rd lumi/man/addAnnotationInfo.Rd lumi/man/addControlData2lumi.Rd lumi/man/addControlData2methyLumiM.Rd lumi/man/addNuID2lumi.Rd lumi/man/adjColorBias.quantile.Rd lumi/man/adjColorBias.ssn.Rd lumi/man/asBigMatrix-methods.Rd lumi/man/beta2m.Rd lumi/man/bgAdjust.Rd lumi/man/bgAdjustMethylation.Rd lumi/man/boxplot-MethyLumiM-methods.Rd lumi/man/boxplot-methods.Rd lumi/man/boxplotColorBias.Rd lumi/man/colorBiasSummary.Rd lumi/man/density-methods.Rd lumi/man/detectOutlier.Rd lumi/man/detectionCall.Rd lumi/man/estimateBeta.Rd lumi/man/estimateIntensity.Rd lumi/man/estimateLumiCV.Rd lumi/man/estimateM.Rd lumi/man/estimateMethylationBG.Rd lumi/man/example.lumi.Rd lumi/man/example.lumiMethy.Rd lumi/man/example.methyTitration.Rd lumi/man/gammaFitEM.Rd lumi/man/getChipInfo.Rd lumi/man/getChrInfo.Rd lumi/man/getControlData.Rd lumi/man/getControlProbe.Rd lumi/man/getControlType.Rd lumi/man/getNuIDMappingInfo.Rd lumi/man/hist-methods.Rd lumi/man/id2seq.Rd lumi/man/importMethyIDAT.Rd lumi/man/inverseVST.Rd lumi/man/is.nuID.Rd lumi/man/lumi.package.Rd lumi/man/lumiB.Rd lumi/man/lumiExpresso.Rd lumi/man/lumiMethyB.Rd lumi/man/lumiMethyC.Rd lumi/man/lumiMethyN.Rd lumi/man/lumiMethyR.Rd lumi/man/lumiMethyStatus.Rd lumi/man/lumiN.Rd lumi/man/lumiQ.Rd lumi/man/lumiR.Rd lumi/man/lumiR.batch.Rd lumi/man/lumiT.Rd lumi/man/m2beta.Rd lumi/man/methylationCall.Rd lumi/man/monoSmu.Rd lumi/man/monoSpline.Rd lumi/man/normalizeMethylation.quantile.Rd lumi/man/normalizeMethylation.ssn.Rd lumi/man/nuID2EntrezID.Rd lumi/man/nuID2IlluminaID.Rd lumi/man/nuID2RefSeqID.Rd lumi/man/nuID2probeID.Rd lumi/man/nuID2targetID.Rd lumi/man/pairs-methods.Rd lumi/man/plot-methods.Rd lumi/man/plotCDF.Rd lumi/man/plotColorBias1D.Rd lumi/man/plotColorBias2D.Rd lumi/man/plotControlData.Rd lumi/man/plotDensity.Rd lumi/man/plotGammaFit.Rd lumi/man/plotHousekeepingGene.Rd lumi/man/plotSampleRelation.Rd lumi/man/plotStringencyGene.Rd lumi/man/plotVST.Rd lumi/man/probeID2nuID.Rd lumi/man/produceGEOPlatformFile.Rd lumi/man/produceGEOSampleInfoTemplate.Rd lumi/man/produceGEOSubmissionFile.Rd lumi/man/produceMethylationGEOSubmissionFile.Rd lumi/man/rankinvariant.Rd lumi/man/rsn.Rd lumi/man/seq2id.Rd lumi/man/smoothQuantileNormalization.Rd lumi/man/ssn.Rd lumi/man/targetID2nuID.Rd lumi/man/vst.Rd
lumi/vignettes
lumi/vignettes/IlluminaAnnotation.R
lumi/vignettes/IlluminaAnnotation.pdf
lumi/vignettes/backup
lumi/vignettes/backup/Control_Probe_Profile.txt
lumi/vignettes/backup/IlluminaAnnotation.Rnw
lumi/vignettes/backup/corConcordanceComparison.png
lumi/vignettes/backup/dataFileSample.png
lumi/vignettes/backup/idMapping.png
lumi/vignettes/backup/lumi.Rnw
lumi/vignettes/backup/lumi_VST_evaluation.Rnw
lumi/vignettes/backup/methylationAnalysis.Rnw
lumi/vignettes/backup/objects-lumi.png
lumi/vignettes/backup/useCaseFlowChart.png
lumi/vignettes/lumi.R
lumi/vignettes/lumi.pdf
lumi/vignettes/lumi_VST_evaluation.R
lumi/vignettes/lumi_VST_evaluation.pdf
lumi/vignettes/methylationAnalysis.R
lumi/vignettes/methylationAnalysis.pdf

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