lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Version 2.28.0

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
Bioconductor views DNAMethylation Microarray OneChannel Preprocessing QualityControl TwoChannel
Date of publicationNone
MaintainerPan Du <dupan.mail@gmail.com>, Lei Huang <lhuang@bsd.uchicago.edu>, Gang Feng <g-feng@northwestern.edu>
LicenseLGPL (>= 2)
Version2.28.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("lumi")

Popular man pages

asBigMatrix-methods: convert the data matrix in the assayData of a ExpressionSet...
beta2m: Convert methylation Beta-value to M-value
m2beta: Convert methylation M-value to Beta-value
plotControlData: Plot the mean expression (with standard deviation bar) of...
rankinvariant: Rank Invariant Normalization
smoothQuantileNormalization: Smooth quantile normalization
ssn: Simple Scaling Normalization
See all...

All man pages Function index File listing

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

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllGenerics.R
R/IlluminaID2nuID.R
R/LumiBatch-class.R
R/addControlData2lumi.R
R/addNuID2lumi.R
R/bgAdjust.R
R/detectOutlier.R
R/detectionCall.R
R/estimateLumiCV.R
R/getChipInfo.R
R/getControlData.R
R/getControlProbe.R
R/getControlType.R
R/getNuIDMappingInfo.R
R/id2seq.R
R/inverseVST.R
R/is.nuID.R
R/lumiB.R
R/lumiExpresso.R
R/lumiN.R
R/lumiQ.R
R/lumiR.R
R/lumiR.batch.R
R/lumiT.R
R/methylation_preprocessing.R
R/monoSmu.R
R/monoSpline.R
R/nuID2EntrezID.R
R/nuID2IlluminaID.R
R/nuID2RefSeqID.R
R/nuIDMapping.R
R/plotCDF.R
R/plotControlData.R
R/plotHousekeepingGene.R
R/plotSampleRelation.R
R/plotStringencyGene.R
R/plotVST.R
R/produceGEOPlatformFile.R
R/produceGEOSampleInfoTemplate.R
R/produceGEOSubmissionFile.R
R/produceMethylationGEOSubmissionFile.R
R/rankinvariant.R
R/rsn.R
R/seq2id.R
R/ssn.R
R/vst.R
R/zzz.R
data
data/datalist
data/example.lumi.rda
data/example.lumiMethy.rda
data/example.methyTitration.rda
inst
inst/CITATION
man
man/IlluminaID2nuID.Rd
man/LumiBatch-class.Rd
man/MAplot-methods.Rd
man/addAnnotationInfo.Rd
man/addControlData2lumi.Rd
man/addControlData2methyLumiM.Rd
man/addNuID2lumi.Rd
man/adjColorBias.quantile.Rd
man/adjColorBias.ssn.Rd
man/asBigMatrix-methods.Rd
man/beta2m.Rd
man/bgAdjust.Rd
man/bgAdjustMethylation.Rd
man/boxplot-MethyLumiM-methods.Rd
man/boxplot-methods.Rd
man/boxplotColorBias.Rd
man/colorBiasSummary.Rd
man/density-methods.Rd
man/detectOutlier.Rd
man/detectionCall.Rd
man/estimateBeta.Rd
man/estimateIntensity.Rd
man/estimateLumiCV.Rd
man/estimateM.Rd
man/estimateMethylationBG.Rd
man/example.lumi.Rd
man/example.lumiMethy.Rd
man/example.methyTitration.Rd
man/gammaFitEM.Rd
man/getChipInfo.Rd
man/getChrInfo.Rd
man/getControlData.Rd
man/getControlProbe.Rd
man/getControlType.Rd
man/getNuIDMappingInfo.Rd
man/hist-methods.Rd
man/id2seq.Rd
man/importMethyIDAT.Rd
man/inverseVST.Rd
man/is.nuID.Rd
man/lumi.package.Rd
man/lumiB.Rd
man/lumiExpresso.Rd
man/lumiMethyB.Rd
man/lumiMethyC.Rd
man/lumiMethyN.Rd
man/lumiMethyR.Rd
man/lumiMethyStatus.Rd
man/lumiN.Rd
man/lumiQ.Rd
man/lumiR.Rd
man/lumiR.batch.Rd
man/lumiT.Rd
man/m2beta.Rd
man/methylationCall.Rd
man/monoSmu.Rd
man/monoSpline.Rd
man/normalizeMethylation.quantile.Rd
man/normalizeMethylation.ssn.Rd
man/nuID2EntrezID.Rd
man/nuID2IlluminaID.Rd
man/nuID2RefSeqID.Rd
man/nuID2probeID.Rd
man/nuID2targetID.Rd
man/pairs-methods.Rd
man/plot-methods.Rd
man/plotCDF.Rd
man/plotColorBias1D.Rd
man/plotColorBias2D.Rd
man/plotControlData.Rd
man/plotDensity.Rd
man/plotGammaFit.Rd
man/plotHousekeepingGene.Rd
man/plotSampleRelation.Rd
man/plotStringencyGene.Rd
man/plotVST.Rd
man/probeID2nuID.Rd
man/produceGEOPlatformFile.Rd
man/produceGEOSampleInfoTemplate.Rd
man/produceGEOSubmissionFile.Rd
man/produceMethylationGEOSubmissionFile.Rd
man/rankinvariant.Rd
man/rsn.Rd
man/seq2id.Rd
man/smoothQuantileNormalization.Rd
man/ssn.Rd
man/targetID2nuID.Rd
man/vst.Rd
vignettes
vignettes/IlluminaAnnotation.R
vignettes/IlluminaAnnotation.pdf
vignettes/lumi.R
vignettes/lumi.pdf
vignettes/lumi_VST_evaluation.R
vignettes/lumi_VST_evaluation.pdf
vignettes/methylationAnalysis.R
vignettes/methylationAnalysis.pdf
lumi documentation built on May 20, 2017, 9:56 p.m.

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