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| methylumi-package | Handle Illumina methylation data |
| betas | methylumi accessors |
| betas,MethyLumiSet-method | Class to hold Illumina Methylation data |
| betas<- | methylumi accessors |
| betas<-,MethyLumiSet,matrix-method | Class to hold Illumina Methylation data |
| boxplot,MethyLumiSet-method | Class to hold Illumina Methylation data |
| combine,MethyLumiSet,MethyLumiSet-method | Class to hold Illumina Methylation data |
| controlTypes | Methods for dealing with control data for Illumina methylation data. |
| controlTypes,MethyLumiQC-method | Class to hold Illumina Methylation QC data |
| controlTypes,MethyLumiSet-method | Class to hold Illumina Methylation data |
| corplot,MethyLumiSet-method | Class to hold Illumina Methylation data |
| exprs,MethyLumiQC-method | Class to hold Illumina Methylation QC data |
| exprs,MethyLumiSet-method | Class to hold Illumina Methylation data |
| exprs<-,MethyLumiQC,matrix-method | Class to hold Illumina Methylation QC data |
| exprs<-,MethyLumiSet,matrix-method | Class to hold Illumina Methylation data |
| extractBarcodeAndPosition | Extract the Barcode and Position Information from Sentrix ID |
| getAssayDataNameSubstitutions | Return a data.frame of AssayData name substitutions. |
| getHistory | methylumi accessors |
| getHistory,MethyLumiSet-method | Class to hold Illumina Methylation data |
| hist,MethyLumiSet-method | Class to hold Illumina Methylation data |
| initialize,MethyLumiQC-method | Class to hold Illumina Methylation QC data |
| initialize,MethyLumiSet-method | Class to hold Illumina Methylation data |
| methylated | methylumi accessors |
| methylated,MethyLumi-method | The base class for storing Illumina Methylation data |
| methylated,MethyLumiSet-method | Class to hold Illumina Methylation data |
| methylated<- | methylumi accessors |
| methylated<-,MethyLumi,matrix-method | The base class for storing Illumina Methylation data |
| methylated<-,MethyLumiSet,matrix-method | Class to hold Illumina Methylation data |
| methylumi | Handle Illumina methylation data |
| MethyLumi-class | The base class for storing Illumina Methylation data |
| MethyLumiQC-class | Class to hold Illumina Methylation QC data |
| methylumiR | Load data from Illumina methylation platform |
| MethyLumiSet-class | Class to hold Illumina Methylation data |
| mldat | Example SAM format Illumina methylation dataset |
| normalizeMethyLumiSet | Normalize a MethyLumiSet, accounting for dye bias |
| pairs,MethyLumiSet-method | Class to hold Illumina Methylation data |
| plotSampleIntensities | Plot the sample intensities. |
| plotSampleIntensities,MethyLumiSet-method | Class to hold Illumina Methylation data |
| pvals | methylumi accessors |
| pvals,MethyLumi-method | The base class for storing Illumina Methylation data |
| pvals<- | methylumi accessors |
| pvals<-,MethyLumi,matrix-method | The base class for storing Illumina Methylation data |
| QCdata | methylumi accessors |
| QCdata,MethyLumiSet-method | Class to hold Illumina Methylation data |
| QCdata<- | methylumi accessors |
| QCdata<-,MethyLumiSet,MethyLumiQC-method | Class to hold Illumina Methylation data |
| QCDataOrNULL-class | Class to hold Illumina Methylation QC data |
| qcplot | Methods for dealing with control data for Illumina methylation data. |
| qcplot,Methylumi-method | The base class for storing Illumina Methylation data |
| qcplot,MethyLumiQC-method | Class to hold Illumina Methylation QC data |
| qcplot,MethyLumiSet-method | Class to hold Illumina Methylation data |
| show,MethyLumiSet-method | Class to hold Illumina Methylation data |
| summary,MethyLumi-method | The base class for storing Illumina Methylation data |
| unmethylated | methylumi accessors |
| unmethylated,MethyLumi-method | The base class for storing Illumina Methylation data |
| unmethylated,MethyLumiSet-method | Class to hold Illumina Methylation data |
| unmethylated<- | methylumi accessors |
| unmethylated<-,MethyLumi,matrix-method | The base class for storing Illumina Methylation data |
| unmethylated<-,MethyLumiSet,matrix-method | Class to hold Illumina Methylation data |
| [,MethyLumiSet-method | Class to hold Illumina Methylation data |