Man pages for seandavi/methylumi
Handle Illumina methylation data
| CpGs | Data frame describing loci on the 27 and 450k arrays. |
| estimateM | Estimate methylation M-value matrix |
| extractBarcodeAndPosition | Extract the Barcode and Position Information from Sentrix ID |
| featureFilter | Annotation-based Filtering of Features (CpG sites) in a... |
| generics | methylumi accessors |
| getAssayDataNameSubstitutions | Return a data.frame of AssayData name substitutions. |
| IDATsToMatrices | convert multiple idats to matrices |
| IDATtoMatrix | process a single IDAT (just the mean intensities) |
| methylData-class | Class '"methylData"', superclass for MethyLumiSet and... |
| MethyLumi-class | The base class for storing Illumina Methylation data |
| methylumIDAT | methylumIDAT |
| methylumiGenerics | Generics defined in methylumi |
| MethyLumiM-class | Class "MethyLumiM": for Illumina Methylation microarray data... |
| methylumi-package | Handle Illumina methylation data |
| MethyLumiQC-class | Class '"MethyLumiQC"' for holding Illumina methylation QC... |
| methylumiR | Load data from Illumina methylation platform |
| MethyLumiSet-class | Class '"MethyLumiSet"' for containing Illumina methylation... |
| mldat | Example SAM format Illumina methylation dataset |
| normalizeMethyLumiSet | Normalize a MethyLumiSet, accounting for dye bias |
| plotSampleIntensities | Plot the sample intensities. |
| qcplot | Methods for dealing with control data for Illumina... |
| stripBeadExtras | Strip excessive probe-level data from MethyLumiSets |
| tcgaPipeline | Total convenience function for processing IDATs like tcga |
| varFilter | Variation-based Filtering of Features (CpG sites) in a... |
