lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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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.

Author
Pan Du, Richard Bourgon, Gang Feng, Simon Lin
Date of publication
None
Maintainer
Pan Du <dupan.mail@gmail.com>
License
LGPL (>= 2)
Version
2.26.3

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