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 |
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 |
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 |
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 |
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) |
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 |
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 |
hist-method | Density plot of a ExpressionSet object |
hist-methods | Density plot of a ExpressionSet object |
hist.ExpressionSet | 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 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 |
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 |
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 |
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 |
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 |
rankinvariant | Rank Invariant Normalization |
rsn | Robust Spline Normalization between chips |
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 |
targetID2nuID | Mapping Illumina TargetID (GeneID) into nuID |
vst | Variance Stabilizing Transformation |
[-method | Class LumiBatch: contain and describe Illumina microarray data |