# BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

## Documentation for package ‘lumi’ version 2.4.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

A B C D E G H I L M N P R S T V misc

lumi-package | A package for preprocessing Illumina microarray data

## -- A --

addColorChannelInfo | Add probe color channel based on the annotation library of Illumina methylation microarray
addControlData2lumi | Add the control probe data into the controlData slot of LumiBatch object
addControlData2methyLumiM | Add methylation control data to a MethyLumiM object
addNuID2lumi | Add the nuID information to the LumiBatch object
addNuId2lumi | Add the nuID information to the LumiBatch object
adjColorBias.quantile | Color bias adjustment of Illumina Infinium methylaton microarrays using smooth quantile normalization
adjColorBias.ssn | Color bias adjustment of Illumina Infinium methylaton microarrays using simple shift and scaling normalization

## -- B --

beadNum | Class LumiBatch: contain and describe Illumina microarray data
beadNum-method | Class LumiBatch: contain and describe Illumina microarray data
beadNum<- | Class LumiBatch: contain and describe Illumina microarray data
beadNum<--method | Class LumiBatch: contain and describe Illumina microarray data
beta2m | Convert methylation Beta-value to M-value
bgAdjust | Background adjustment for Illumina data
bgAdjustMethylation | Estimate and adjust the background levels of Illumina Infinium methylaton microarrays
boxplot-method | boxplot of a MethyLumiM object
boxplot-method | boxplot of a ExpressionSet object
boxplot-methods | boxplot of a ExpressionSet object
boxplot.ExpressionSet | boxplot of a ExpressionSet object
boxplotColorBias | Plot the Illumina Infinium methylation color bias in terms of boxplot

## -- C --

class:LumiBatch | Class LumiBatch: contain and describe Illumina microarray data
colorBiasSummary | A summary of colorBias information
combine-method | Class LumiBatch: contain and describe Illumina microarray data
controlData | Class LumiBatch: contain and describe Illumina microarray data
controlData-method | Class LumiBatch: contain and describe Illumina microarray data
controlData<- | Class LumiBatch: contain and describe Illumina microarray data
controlData<--method | Class LumiBatch: contain and describe Illumina microarray data

## -- D --

density-method | Density plot of a ExpressionSet object
density-methods | Density plot of a ExpressionSet object
density.ExpressionSet | Density plot of a ExpressionSet object
detection | Class LumiBatch: contain and describe Illumina microarray data
detection-method | Class LumiBatch: contain and describe Illumina microarray data
detection<- | Class LumiBatch: contain and describe Illumina microarray data
detection<--method | Class LumiBatch: contain and describe Illumina microarray data
detectionCall | Estimate the detectable probe ratio
detectOutlier | Detect the outlier sample (or gene)

## -- E --

estimateBeta | Estimate methylation Beta-value matrix
estimateIntensity | Estimate intensity of Illumina methylation data
estimateLumiCV | Estimate the coefficient of variance matrix of LumiBatch object
estimateM | Estimate methylation M-value matrix
estimateMethylationBG | Estimate the background levels of Illumina Infinium methylaton microarrays
example.lumi | Example Illumina Expression data in LumiBatch class
example.lumiMethy | Example Illumina Infinium Methylation data in MethyLumiM class
example.methyTitration | Example Illumina Infinium Methylation titration data in MethyLumiM class

## -- G --

gammaFitEM | Estimate the methylation status by fitting a Gamma mixture model using EM algorithm
getChipInfo | Get Illumina Chip Information based on probe identifiers
getControlData | Get control probe information
getControlProbe | Get the control probe Ids
getControlType | Get the types of the control probes
getHistory | Class LumiBatch: contain and describe Illumina microarray data
getHistory-method | Class LumiBatch: contain and describe Illumina microarray data
getNuIDMappingInfo | get the mapping information from nuID to RefSeq ID

## -- H --

hist-method | Density plot of a ExpressionSet object
hist-methods | Density plot of a ExpressionSet object
hist.ExpressionSet | Density plot of a ExpressionSet object

## -- I --

id2seq | Transfer a nuID as a nucleotide sequence
IlluminaID2nuID | Matching Illumina IDs to nuID based on Illumina ID mapping library
initialize-method | Class LumiBatch: contain and describe Illumina microarray data
inverseVST | Inverse VST transform
is.nuID | nuID self-identification

## -- L --

lumi | A package for preprocessing Illumina microarray data
lumiB | Background correction of Illumina Expression data
LumiBatch | Class LumiBatch: contain and describe Illumina microarray data
LumiBatch-class | Class LumiBatch: contain and describe Illumina microarray data
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 sites
lumiN | Between chip normalization of a LumiBatch object
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

## -- M --

m2beta | Convert methylation M-value to Beta-value
MAplot | MAplot of a ExpressionSet object
MAplot-method | MAplot of a ExpressionSet object
MAplot-methods | MAplot of a ExpressionSet object
MAplot.ExpressionSet | MAplot of a ExpressionSet object
methylationCall | Estimated methylation call
monoSmu | Monotonic smooth method
monoSpline | Fitting a curve with monotonic spline

## -- N --

normalizeMethylation.quantile | Quantile normalization of Illumina Infinium methylation data at probe level
normalizeMethylation.ssn | Shift and scaling normalization of Illumina Infinium methylation data at probe level
nuID2EntrezID | Map nuID to Entrez ID
nuID2IlluminaID | Matching nuIDs to Illumina IDs based on Illumina ID mapping library
nuID2probeID | Mapping nuID into Illumina ProbeID
nuID2RefSeqID | Map nuID to RefSeq ID
nuID2targetID | Mapping nuID into Illumina TargetID

## -- P --

pairs-method | Pair plot of an ExpressionSet object
pairs-methods | Pair plot of an ExpressionSet object
pairs.ExpressionSet | Pair plot of an ExpressionSet object
plot-method | Plot of a ExpressionSet object
plot-methods | Plot of a ExpressionSet object
plot.ExpressionSet | Plot of a ExpressionSet object
plotCDF | plot the cumulative distribution function of a ExpressionSet object
plotCDF-method | plot the cumulative distribution function of a ExpressionSet object
plotCDF.ExpressionSet | plot the cumulative distribution function of a ExpressionSet object
plotColorBias1D | Plot the color bias density plot of Illumina Infinium Methylation data
plotColorBias2D | Plot the color bias of Illumina Infinium Methylation data in two dimensions
plotControlData | Plot the mean expression (with standard deviation bar) of different type of control probes
plotDensity | plot the density distribution
plotDensity.ExpressionSet | plot the density distribution
plotGammaFit | plot the fitting results of 'gammaFitEM'
plotHousekeepingGene | Plot the housekeeping gene expression profile
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 microarray data in SOFT format

## -- R --

rankinvariant | Rank Invariant Normalization
rsn | Robust Spline Normalization between chips

## -- S --

sampleNames<--method | Class LumiBatch: contain and describe Illumina microarray data
se.exprs | Class LumiBatch: contain and describe Illumina microarray data
se.exprs-method | Class LumiBatch: contain and describe Illumina microarray data
se.exprs<- | Class LumiBatch: contain and describe Illumina microarray data
se.exprs<--method | Class LumiBatch: contain and describe Illumina microarray data
seq2id | Transfer a nucleotide sequence as a nuID
show-method | Class LumiBatch: contain and describe Illumina microarray data
smoothQuantileNormalization | Smooth quantile normalization
ssn | Simple Scaling Normalization
summary-method | Class LumiBatch: contain and describe Illumina microarray data

## -- T --

targetID2nuID | Mapping Illumina TargetID (GeneID) into nuID

## -- V --

vst | Variance Stabilizing Transformation

## -- misc --

[-method | Class LumiBatch: contain and describe Illumina microarray data