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| minfi-package | Analyze Illumina's methylation arrays |
| bgcorrect.illumina | Perform preprocessing as Genome Studio. |
| controlStripPlot | Plot control probe signals. |
| densityBeanPlot | Density bean plots of methylation Beta values. |
| densityPlot | Density plots of methylation Beta values. |
| detectionP | Detection p-values for all probed genomic positions. |
| dmpFinder | Find differentially methylated positions |
| getAnno | Class MethylSet |
| getBeta | Class MethylSet |
| getControlAddress | Utility functions for retrieving array design information for Illumina methylation microarrays. |
| getGreen | Class '"RGChannelSet"' |
| getM | Class MethylSet |
| getManifest | Class '"RGChannelSet"' |
| getManifestInfo | Utility functions for retrieving array design information for Illumina methylation microarrays. |
| getMeth | Class MethylSet |
| getProbeData | Utility functions for retrieving array design information for Illumina methylation microarrays. |
| getProbeInfo | Utility functions for retrieving array design information for Illumina methylation microarrays. |
| getRed | Class '"RGChannelSet"' |
| getUnmeth | Class MethylSet |
| IlluminaMethylationManifest-class | Class '"IlluminaMethylationManifest"' |
| ilogit2 | logit in base 2. |
| initialize-method | Class MethylSet |
| initialize-method | Class '"RGChannelSet"' |
| logit2 | logit in base 2. |
| manifestNew | Class '"IlluminaMethylationManifest"' |
| mdsPlot | Multi-dimensional scaling plots giving an overview of similarities and differences between samples. |
| MethylSet-class | Class MethylSet |
| minfi | Analyze Illumina's methylation arrays |
| normalize.illumina.control | Perform preprocessing as Genome Studio. |
| plotCpg | Plot methylation values at an single genomic position |
| preprocessIllumina | Perform preprocessing as Genome Studio. |
| preprocessRaw | Creation of a MethylSet without normalization |
| qcReport | QC report for Illumina Infinium Human Methylation 450k arrays |
| read.450k | Parsing IDAT files from Illumina methylation arrays. |
| read.450k.exp | Reads an entire 450k experiment using a sample sheet |
| read.450k.sheet | Reading an Illumina methylation sample sheet |
| RGChannelSet-class | Class '"RGChannelSet"' |
| RGChannelSetExtended-class | Class '"RGChannelSet"' |
| show-method | Class '"IlluminaMethylationManifest"' |
| show-method | Class MethylSet |
| show-method | Class '"RGChannelSet"' |