BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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Documentation for package ‘lumi’ version 2.40.0

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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 --

addAnnotationInfo Add probe color channel and basic annotation information 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
asBigMatrix convert the data matrix in the assayData of a ExpressionSet as BigMatrix
asBigMatrix-method convert the data matrix in the assayData of a ExpressionSet as BigMatrix
asBigMatrix-methods convert the data matrix in the assayData of a ExpressionSet as BigMatrix

-- 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
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
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
importMethyIDAT Import Illumina methylation .idat files as an MethyLumiM object
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