Man pages for lumi
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

addAnnotationInfoAdd probe color channel and basic annotation information...
addControlData2lumiAdd the control probe data into the controlData slot of...
addControlData2methyLumiMAdd methylation control data to a MethyLumiM object
addNuID2lumiAdd the nuID information to the LumiBatch object
adjColorBias.quantileColor bias adjustment of Illumina Infinium methylaton...
adjColorBias.ssnColor bias adjustment of Illumina Infinium methylaton...
asBigMatrix-methodsconvert the data matrix in the assayData of a ExpressionSet...
beta2mConvert methylation Beta-value to M-value
bgAdjustBackground adjustment for Illumina data
bgAdjustMethylationEstimate and adjust the background levels of Illumina...
boxplotColorBiasPlot the Illumina Infinium methylation color bias in terms of...
boxplot-methodsboxplot of a ExpressionSet object
boxplot-MethyLumiM-methodsboxplot of a MethyLumiM object
colorBiasSummaryA summary of colorBias information
density-methodsDensity plot of a ExpressionSet object
detectionCallEstimate the detectable probe ratio
detectOutlierDetect the outlier sample (or gene)
estimateBetaEstimate methylation Beta-value matrix
estimateIntensityEstimate intensity of Illumina methylation data
estimateLumiCVEstimate the coefficient of variance matrix of LumiBatch...
estimateMEstimate methylation M-value matrix
estimateMethylationBGEstimate the background levels of Illumina Infinium...
example.lumiExample Illumina Expression data in LumiBatch class
example.lumiMethyExample Illumina Infinium Methylation data in MethyLumiM...
example.methyTitrationExample Illumina Infinium Methylation titration data in...
gammaFitEMEstimate the methylation status by fitting a Gamma mixture...
getChipInfoGet Illumina Chip Information based on probe identifiers
getChrInfoget the chromosome location information of methylation probes
getControlDataGet control probe information
getControlProbeGet the control probe Ids
getControlTypeGet the types of the control probes
getNuIDMappingInfoget the mapping information from nuID to RefSeq ID
hist-methodsDensity plot of a ExpressionSet object
id2seqTransfer a nuID as a nucleotide sequence
IlluminaID2nuIDMatching Illumina IDs to nuID based on Illumina ID mapping...
importMethyIDATImport Illumina methylation .idat files as an MethyLumiM...
inverseVSTInverse VST transform
is.nuIDnuID self-identification
lumiBBackground correction of Illumina Expression data
LumiBatch-classClass LumiBatch: contain and describe Illumina microarray...
lumiExpressoFrom raw Illumina probe intensities to expression values
lumiMethyBAdjust background level of Illumina Infinium methylation data
lumiMethyCColor bias adjust of Illumina Infinium methylation data
lumiMethyNNormalize the Illumina Infinium methylation data
lumiMethyRReading Illumina methylation microarray data
lumiMethyStatusEstimate the methylation status of individual methylation...
lumiNBetween chip normalization of a LumiBatch object
lumi.packageA package for preprocessing Illumina microarray data
lumiQQuality control evaluation of the LumiBatch object
lumiRRead in Illumina expression data
lumiR.batchRead BeadStudio output files in batch
lumiTTransfer the Illumina data to stabilize the variance
m2betaConvert methylation M-value to Beta-value
MAplot-methodsMAplot of a ExpressionSet object
methylationCallEstimated methylation call
monoSmuMonotonic smooth method
monoSplineFitting a curve with monotonic spline
normalizeMethylation.quantileQuantile normalization of Illumina Infinium methylation data...
normalizeMethylation.ssnShift and scaling normalization of Illumina Infinium...
nuID2EntrezIDMap nuID to Entrez ID
nuID2IlluminaIDMatching nuIDs to Illumina IDs based on Illumina ID mapping...
nuID2probeIDMapping nuID into Illumina ProbeID
nuID2RefSeqIDMap nuID to RefSeq ID
nuID2targetIDMapping nuID into Illumina TargetID
pairs-methodsPair plot of an ExpressionSet object
plotCDFplot the cumulative distribution function of a ExpressionSet...
plotColorBias1DPlot the color bias density plot of Illumina Infinium...
plotColorBias2DPlot the color bias of Illumina Infinium Methylation data in...
plotControlDataPlot the mean expression (with standard deviation bar) of...
plotDensityplot the density distribution
plotGammaFitplot the fitting results of 'gammaFitEM'
plotHousekeepingGenePlot the housekeeping gene expression profile
plot-methodsPlot of a ExpressionSet object
plotSampleRelationvisualize the sample relations
plotStringencyGeneplot the Stringency related control probe profiles
plotVSTplot the VST (Variance Stabilizing Transform) function
probeID2nuIDMapping Illumina ProbeID as nuID
produceGEOPlatformFileProduce GEO Platform Submission File in SOFT format
produceGEOSampleInfoTemplateProduce the template of GEO sample information
produceGEOSubmissionFileProduce GEO Sample Submission File in SOFT format
produceMethylationGEOSubmissionFileProduce GEO Sample Submission File of Illumina methylation...
rankinvariantRank Invariant Normalization
rsnRobust Spline Normalization between chips
seq2idTransfer a nucleotide sequence as a nuID
smoothQuantileNormalizationSmooth quantile normalization
ssnSimple Scaling Normalization
targetID2nuIDMapping Illumina TargetID (GeneID) into nuID
vstVariance Stabilizing Transformation
lumi documentation built on Nov. 1, 2018, 3:29 a.m.