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| minfi-package | Analyze Illumina's methylation arrays |
| addQC | Estimate sample-specific quality control (QC) for methylation data |
| addSex | Estimating sample sex based on methylation data |
| addSnpInfo | Accessing annotation for Illumina methylation objects |
| annotation-method | GenomicMethylSet instances |
| annotation-method | GenomicRatioSet instances |
| bgcorrect.illumina | Perform preprocessing as Genome Studio. |
| blockFinder | Finds blocks of methylation differences for Illumina methylation arrays |
| bumphunter-method | Methods for function 'bumphunter' in Package 'minfi' |
| combine-method | GenomicMethylSet instances |
| combine-method | GenomicRatioSet instances |
| combine-method | MethylSet instances |
| combine-method | Class '"RGChannelSet"' |
| combine-method | RatioSet instances |
| combineArrays | A method for combining different types of methylation arrays into a virtual array. |
| combineArrays-method | A method for combining different types of methylation arrays into a virtual array. |
| compartments | Estimates A/B compartments from Illumina methylation arrays |
| controlStripPlot | Plot control probe signals. |
| convertArray | A method for converting a type of methylation arrays into a virtual array of another type. |
| convertArray-method | A method for converting a type of methylation arrays into a virtual array of another type. |
| cpgCollapse | Collapse methylation values of adjacent CpGs into a summary value. |
| createCorMatrix | Estimates A/B compartments from Illumina methylation arrays |
| 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 |
| dropLociWithSnps | Accessing annotation for Illumina methylation objects |
| dropMethylationLoci | MethylSet instances |
| estimateCellCounts | Cell Proportion Estimation |
| extractAB | Estimates A/B compartments from Illumina methylation arrays |
| featureNames-method | GenomicMethylSet instances |
| featureNames-method | GenomicRatioSet instances |
| fixMethOutliers | Fix methylation outliers |
| gaphunter | Find gap signals in 450k data |
| GenomicMethylSet | GenomicMethylSet instances |
| GenomicMethylSet-class | GenomicMethylSet instances |
| GenomicRatioSet | GenomicRatioSet instances |
| GenomicRatioSet-class | GenomicRatioSet instances |
| getAnnotation | Accessing annotation for Illumina methylation objects |
| getAnnotationObject | Accessing annotation for Illumina methylation objects |
| getBeta | MethylSet instances |
| getBeta-method | GenomicMethylSet instances |
| getBeta-method | GenomicRatioSet instances |
| getBeta-method | MethylSet instances |
| getBeta-method | Class '"RGChannelSet"' |
| getBeta-method | RatioSet instances |
| getCN | GenomicRatioSet instances |
| getCN-method | GenomicMethylSet instances |
| getCN-method | GenomicRatioSet instances |
| getCN-method | MethylSet instances |
| getCN-method | RatioSet instances |
| getControlAddress | Class '"IlluminaMethylationManifest"' |
| getControlTypes | Class '"IlluminaMethylationManifest"' |
| getGenomicRatioSetFromGEO | Reading Illumina methylation array data from GEO. |
| getGreen | Class '"RGChannelSet"' |
| getIslandStatus | Accessing annotation for Illumina methylation objects |
| getLocations | Accessing annotation for Illumina methylation objects |
| getM | MethylSet instances |
| getM-method | GenomicMethylSet instances |
| getM-method | GenomicRatioSet instances |
| getM-method | MethylSet instances |
| getM-method | RatioSet 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 |
| getMethSignal | Various utilities |
| getOOB | Class '"RGChannelSet"' |
| getProbeInfo | Class '"IlluminaMethylationManifest"' |
| getProbeType | Accessing annotation for Illumina methylation objects |
| getQC | Estimate sample-specific quality control (QC) for methylation data |
| getRed | Class '"RGChannelSet"' |
| getSex | Estimating sample sex based on methylation data |
| getSnpBeta | Class '"RGChannelSet"' |
| getSnpInfo | Accessing annotation for Illumina methylation objects |
| 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"' |
| initialize-method | RatioSet instances |
| logit2 | logit in base 2. |
| makeGenomicRatioSetFromMatrix | Make a GenomicRatioSet from a matrix |
| mapToGenome | Mapping methylation data to the genome |
| mapToGenome-method | GenomicMethylSet instances |
| mapToGenome-method | GenomicRatioSet instances |
| 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 |
| minfi-defunct | Defunct functions in package 'minfi' |
| minfi-deprecated | Deprecated functions in package 'minfi' |
| minfiQC | easy one-step QC of methylation object |
| 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 |
| plotQC | Estimate sample-specific quality control (QC) for methylation data |
| plotSex | Estimating sample sex based on methylation data |
| preprocessFunnorm | Functional normalization for Illumina 450k arrays |
| preprocessIllumina | Perform preprocessing as Genome Studio. |
| preprocessMethod | MethylSet instances |
| preprocessMethod-method | GenomicMethylSet instances |
| preprocessMethod-method | GenomicRatioSet instances |
| preprocessMethod-method | MethylSet instances |
| preprocessMethod-method | RatioSet instances |
| preprocessNoob | The Noob/ssNoob preprocessing method for Infinium methylation microarrays. |
| preprocessQuantile | Stratified quantile normalization for an Illumina methylation array. |
| 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 |
| ratioConvert | Converting methylation signals to ratios (Beta or M-values) |
| ratioConvert-method | Converting methylation signals to ratios (Beta or M-values) |
| ratioConvert-methods | Converting methylation signals to ratios (Beta or M-values) |
| RatioSet | RatioSet instances |
| RatioSet-class | RatioSet instances |
| read.450k | Defunct functions in package 'minfi' |
| read.450k.exp | Defunct functions in package 'minfi' |
| read.450k.sheet | Defunct functions in package 'minfi' |
| read.metharray | Parsing IDAT files from Illumina methylation arrays. |
| read.metharray.exp | Reads an entire metharray experiment using a sample sheet |
| read.metharray.sheet | Reading an Illumina methylation sample sheet |
| readGEORawFile | Read in Unmethylated and Methylated signals from a GEO raw file. |
| readTCGA | Read in tab deliminited file in the TCGA format |
| 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"' |
| show-method | RatioSet instances |
| subsetByLoci | Subset an RGChannelset by CpG loci. |