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