Man pages for kasperdanielhansen/minfi
Analyze Illumina Infinium DNA methylation arrays
| blockFinder | Finds blocks of methylation differences for Illumina... |
| bumphunter | Methods for function 'bumphunter' in Package 'minfi' |
| combineArrays | A method for combining different types of methylation arrays... |
| 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... |
| cpgCollapse | Collapse methylation values of adjacent CpGs into a summary... |
| DelayedArray_utils | Stubs for internal functions |
| 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 |
| estimateCellCounts | Cell Proportion Estimation |
| fixMethOutliers | Fix methylation outliers |
| gaphunter | Find gap signals in 450k data |
| GenomicMethylSet-class | GenomicMethylSet instances |
| GenomicRatioSet-class | GenomicRatioSet instances |
| getAnnotation | Accessing annotation for Illumina methylation objects |
| getGenomicRatioSetFromGEO | Reading Illumina methylation array data from GEO. |
| getQC | Estimate sample-specific quality control (QC) for methylation... |
| getSex | Estimating sample sex based on methylation data |
| IlluminaMethylationAnnotation-class | Class 'IlluminaMethylationAnnotation' |
| IlluminaMethylationManifest-class | Class '"IlluminaMethylationManifest"' |
| logit2 | logit in base 2. |
| makeGenomicRatioSetFromMatrix | Make a GenomicRatioSet from a matrix |
| mapToGenome-methods | Mapping methylation data to the genome |
| mdsPlot | Multi-dimensional scaling plots giving an overview of... |
| MethylSet-class | MethylSet instances |
| minfi-defunct | Defunct functions in package 'minfi' |
| minfi-deprecated | Deprecated functions in package 'minfi' |
| minfi-package | Analyze Illumina's methylation arrays |
| minfiQC | easy one-step QC of methylation object |
| plotBetasByType | Plot the overall distribution of beta values and the... |
| plotCpg | Plot methylation values at an single genomic position |
| preprocessFunnorm | Functional normalization for Illumina 450k arrays |
| preprocessIllumina | Perform preprocessing as Genome Studio. |
| preprocessNoob | The Noob/ssNoob preprocessing method for Infinium methylation... |
| preprocessQuantile | Stratified quantile normalization for an Illumina methylation... |
| preprocessRaw | Creation of a MethylSet without normalization |
| preprocessSwan | Subset-quantile Within Array Normalisation for Illumina... |
| qcReport | QC report for Illumina Infinium Human Methylation 450k arrays |
| ratioConvert-methods | Converting methylation signals to ratios (Beta or M-values) |
| RatioSet-class | RatioSet instances |
| readGEORawFile | Read in Unmethylated and Methylated signals from a GEO raw... |
| 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 |
| readTCGA | Read in tab deliminited file in the TCGA format |
| RGChannelSet-class | Class '"RGChannelSet"' |
| subsetByLoci | Subset an RGChannelset by CpG loci. |
| utils | Various utilities |
