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| minfi-package | Analyze Illumina's methylation arrays |
| annotation-method | GenomicMethylSet instances |
| annotation-method | GenomicRatioSet instances |
| 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 |
| dropMethylationLoci | MethylSet instances |
| featureNames-method | GenomicMethylSet instances |
| featureNames-method | GenomicRatioSet instances |
| GenomicMethylSet | GenomicMethylSet instances |
| GenomicMethylSet-class | GenomicMethylSet instances |
| GenomicRatioSet | GenomicRatioSet instances |
| GenomicRatioSet-class | GenomicRatioSet instances |
| getBeta | MethylSet instances |
| getBeta-method | GenomicMethylSet instances |
| getBeta-method | GenomicRatioSet instances |
| getBeta-method | MethylSet instances |
| getBeta-method | Class '"RGChannelSet"' |
| getCN | GenomicRatioSet instances |
| getCN-method | GenomicRatioSet instances |
| getControlAddress | Class '"IlluminaMethylationManifest"' |
| getControlTypes | Class '"IlluminaMethylationManifest"' |
| getGreen | Class '"RGChannelSet"' |
| getLocations | Class 'IlluminaMethylationAnnotation' |
| getLocations-method | Class 'IlluminaMethylationAnnotation' |
| getLocations-method | MethylSet instances |
| getM | MethylSet instances |
| getM-method | GenomicMethylSet instances |
| getM-method | GenomicRatioSet instances |
| getM-method | MethylSet instances |
| getManifest | Class '"IlluminaMethylationManifest"' |
| getManifest-method | Class 'IlluminaMethylationAnnotation' |
| getManifest-method | Class '"IlluminaMethylationManifest"' |
| getManifest-method | MethylSet instances |
| getManifest-method | Class '"RGChannelSet"' |
| getManifestInfo | Class '"IlluminaMethylationManifest"' |
| getMeth | MethylSet instances |
| getMeth-method | GenomicMethylSet instances |
| getMeth-method | MethylSet instances |
| getProbeInfo | Class '"IlluminaMethylationManifest"' |
| getRed | Class '"RGChannelSet"' |
| getUnmeth | MethylSet instances |
| getUnmeth-method | GenomicMethylSet instances |
| getUnmeth-method | MethylSet instances |
| IlluminaMethylationAnnotation | Class 'IlluminaMethylationAnnotation' |
| IlluminaMethylationAnnotation-class | Class 'IlluminaMethylationAnnotation' |
| IlluminaMethylationManifest | Class '"IlluminaMethylationManifest"' |
| IlluminaMethylationManifest-class | Class '"IlluminaMethylationManifest"' |
| ilogit2 | logit in base 2. |
| initialize-method | MethylSet instances |
| initialize-method | Class '"RGChannelSet"' |
| logit2 | logit in base 2. |
| mapToGenome | Mapping methylation data to the genome |
| mapToGenome-method | Mapping methylation data to the genome |
| mapToGenome-methods | Mapping methylation data to the genome |
| mdsPlot | Multi-dimensional scaling plots giving an overview of similarities and differences between samples. |
| MethylSet | MethylSet instances |
| MethylSet-class | MethylSet instances |
| minfi | Analyze Illumina's methylation arrays |
| normalize.illumina.control | Perform preprocessing as Genome Studio. |
| pData-method | GenomicMethylSet instances |
| pData-method | GenomicRatioSet instances |
| plotBetasByType | Plot the overall distribution of beta values and the distributions of the Infinium I and II probe types. |
| plotCpg | Plot methylation values at an single genomic position |
| preprocessIllumina | Perform preprocessing as Genome Studio. |
| preprocessMethod | MethylSet instances |
| preprocessMethod-method | GenomicMethylSet instances |
| preprocessMethod-method | GenomicRatioSet instances |
| preprocessMethod-method | MethylSet instances |
| preprocessRaw | Creation of a MethylSet without normalization |
| preprocessSWAN | Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips |
| 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 '"RGChannelSet"' |
| RGChannelSet-class | Class '"RGChannelSet"' |
| RGChannelSetExtended | Class '"RGChannelSet"' |
| RGChannelSetExtended-class | Class '"RGChannelSet"' |
| sampleNames-method | GenomicMethylSet instances |
| sampleNames-method | GenomicRatioSet instances |
| show-method | GenomicMethylSet instances |
| show-method | GenomicRatioSet instances |
| show-method | Class 'IlluminaMethylationAnnotation' |
| show-method | Class '"IlluminaMethylationManifest"' |
| show-method | MethylSet instances |
| show-method | Class '"RGChannelSet"' |