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

Files in this package

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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