Analyze Illumina's 450k methylation arrays


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Documentation for package ‘minfi’ version 1.6.0

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minfi-package Analyze Illumina's methylation arrays
annotation-method GenomicMethylSet instances
annotation-method GenomicRatioSet instances
bgcorrect.illumina Perform preprocessing as Genome Studio.
controlStripPlot Plot control probe signals.
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
featureNames-method GenomicMethylSet instances
featureNames-method GenomicRatioSet instances
GenomicMethylSet GenomicMethylSet instances
GenomicMethylSet-class GenomicMethylSet instances
GenomicRatioSet GenomicRatioSet instances
GenomicRatioSet-class GenomicRatioSet instances
getBeta MethylSet instances
getBeta-method GenomicMethylSet instances
getBeta-method GenomicRatioSet instances
getBeta-method MethylSet instances
getBeta-method Class '"RGChannelSet"'
getCN GenomicRatioSet instances
getCN-method GenomicRatioSet instances
getControlAddress Class '"IlluminaMethylationManifest"'
getControlTypes Class '"IlluminaMethylationManifest"'
getGreen Class '"RGChannelSet"'
getLocations Class 'IlluminaMethylationAnnotation'
getLocations-method Class 'IlluminaMethylationAnnotation'
getLocations-method MethylSet instances
getM MethylSet instances
getM-method GenomicMethylSet instances
getM-method GenomicRatioSet instances
getM-method MethylSet 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
getProbeInfo Class '"IlluminaMethylationManifest"'
getRed Class '"RGChannelSet"'
getUnmeth MethylSet instances
getUnmeth-method GenomicMethylSet instances
getUnmeth-method MethylSet instances
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"'
logit2 logit in base 2.
mapToGenome Mapping methylation data to the genome
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
normalize.illumina.control Perform preprocessing as Genome Studio.
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
preprocessIllumina Perform preprocessing as Genome Studio.
preprocessMethod MethylSet instances
preprocessMethod-method GenomicMethylSet instances
preprocessMethod-method GenomicRatioSet instances
preprocessMethod-method MethylSet instances
preprocessRaw Creation of a MethylSet without normalization
preprocessSWAN Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips
qcReport QC report for Illumina Infinium Human Methylation 450k arrays
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"'
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"'