# Analyze Illumina Infinium DNA methylation arrays

## Documentation for package ‘minfi’ version 1.22.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I L M N P Q R S

minfi-package | Analyze Illumina's methylation arrays

## -- A --

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
annotation-method | MethylSet instances
annotation-method | Class '"RGChannelSet"'
annotation-method | RatioSet instances
annotation<--method | GenomicMethylSet instances
annotation<--method | GenomicRatioSet instances
annotation<--method | MethylSet instances
annotation<--method | Class '"RGChannelSet"'
annotation<--method | RatioSet instances

## -- B --

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'

## -- C --

coerce-method | Class '"RGChannelSet"'
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

## -- D --

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

## -- E --

estimateCellCounts | Cell Proportion Estimation
extractAB | Estimates A/B compartments from Illumina methylation arrays

## -- F --

featureNames-method | GenomicMethylSet instances
featureNames-method | GenomicRatioSet instances
featureNames-method | MethylSet instances
featureNames-method | Class '"RGChannelSet"'
featureNames-method | RatioSet instances
featureNames<--method | GenomicMethylSet instances
featureNames<--method | GenomicRatioSet instances
featureNames<--method | MethylSet instances
featureNames<--method | Class '"RGChannelSet"'
featureNames<--method | RatioSet instances
fixMethOutliers | Fix methylation outliers

## -- G --

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"'
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
getNBeads | Class '"RGChannelSet"'
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

## -- I --

IlluminaMethylationAnnotation | Class 'IlluminaMethylationAnnotation'
IlluminaMethylationAnnotation-class | Class 'IlluminaMethylationAnnotation'
IlluminaMethylationManifest | Class '"IlluminaMethylationManifest"'
IlluminaMethylationManifest-class | Class '"IlluminaMethylationManifest"'
ilogit2 | logit in base 2.

## -- L --

logit2 | logit in base 2.

## -- M --

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

## -- N --

normalize.illumina.control | Perform preprocessing as Genome Studio.

## -- P --

pData-method | GenomicMethylSet instances
pData-method | GenomicRatioSet instances
pData-method | MethylSet instances
pData-method | Class '"RGChannelSet"'
pData-method | RatioSet instances
pData<--method | GenomicMethylSet instances
pData<--method | GenomicRatioSet instances
pData<--method | MethylSet instances
pData<--method | Class '"RGChannelSet"'
pData<--method | RatioSet 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

## -- Q --

qcReport | QC report for Illumina Infinium Human Methylation 450k arrays

## -- R --

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"'

## -- S --

sampleNames-method | GenomicMethylSet instances
sampleNames-method | GenomicRatioSet instances
sampleNames-method | MethylSet instances
sampleNames-method | Class '"RGChannelSet"'
sampleNames-method | RatioSet instances
sampleNames<--method | GenomicMethylSet instances
sampleNames<--method | GenomicRatioSet instances
sampleNames<--method | MethylSet instances
sampleNames<--method | Class '"RGChannelSet"'
sampleNames<--method | RatioSet 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.