Analyze Illumina's 450k methylation arrays


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Documentation for package ‘minfi’ version 1.8.9

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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

-- 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 --

controlStripPlot Plot control probe signals.
cpgCollapse Collapse methylation values of adjacent CpGs into a summary value.

-- 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
dropMethylationLoci MethylSet instances

-- E --

estimateCellCounts Cell Proportion Estimation

-- F --

featureNames-method GenomicMethylSet instances
featureNames-method GenomicRatioSet instances
fixMethOutliers Fix methylation outliers

-- G --

GenomicMethylSet GenomicMethylSet instances
GenomicMethylSet-class GenomicMethylSet instances
GenomicRatioSet GenomicRatioSet instances
GenomicRatioSet-class GenomicRatioSet instances
getAnnotation 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"'
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
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
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.
initialize-method MethylSet instances
initialize-method Class '"RGChannelSet"'
initialize-method RatioSet instances

-- L --

logit2 logit in base 2.

-- M --

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
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
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
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
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 Parsing IDAT files from Illumina methylation arrays.
read.450k.exp Reads an entire 450k experiment using a sample sheet
read.450k.sheet Reading an Illumina methylation sample sheet
RGChannelSet Class '"RGChannelSet"'
RGChannelSet-class Class '"RGChannelSet"'
RGChannelSetExtended Class '"RGChannelSet"'
RGChannelSetExtended-class Class '"RGChannelSet"'

-- S --

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