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| missMethyl-package | Introduction to the missMethyl package |
| contrasts.varFit | Compute contrasts for a varFit object. |
| densityByProbeType | Plot the beta value distributions of the Infinium I and II probe types relative to the overall beta value distribution. |
| getINCs | Extract intensity data for 613 Illumina negative controls found on 450k arrays. |
| getLeveneResiduals | Obtain Levene residuals |
| getMappedEntrezIDs | Get mapped Entrez Gene IDs from CpG probe names |
| gometh | Gene ontology testing for Ilumina methylation array data |
| gsameth | Generalised gene set testing for Illumina's methylation array data |
| missMethyl | Introduction to the missMethyl package |
| RUVadj | Adjust estimated variances |
| RUVfit | Remove unwanted variation when testing for differential methylation |
| SWAN | Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips |
| SWAN.default | Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips |
| SWAN.MethyLumiSet | Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips |
| SWAN.RGChannelSet | Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips |
| topGSA | Get table of top 20 enriched pathways |
| topRUV | Table of top-ranked differentially methylated CpGs obatained from a differential methylation analysis using RUV |
| topVar | Table of top-ranked differentially variable CpGs |
| varFit | Testing for differential variability |
| varFit.default | Testing for differential variability |
| varFit.DGEList | Testing for differential variability |
| varFit.MethylSet | Testing for differential variability |