Analyze Illumina Infinium DNA methylation arrays

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Documentation for package ‘minfi’ version 1.55.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
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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.