Analyze Illumina Infinium DNA methylation arrays


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Documentation for package ‘minfi’ version 1.55.1

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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.