Analyze Illumina's 450k methylation arrays


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Documentation for package ‘minfi’ version 1.2.0

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minfi-package Analyze Illumina's methylation arrays
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
getAnno Class MethylSet
getBeta Class MethylSet
getControlAddress Utility functions for retrieving array design information for Illumina methylation microarrays.
getGreen Class '"RGChannelSet"'
getM Class MethylSet
getManifest Class '"RGChannelSet"'
getManifestInfo Utility functions for retrieving array design information for Illumina methylation microarrays.
getMeth Class MethylSet
getProbeData Utility functions for retrieving array design information for Illumina methylation microarrays.
getProbeInfo Utility functions for retrieving array design information for Illumina methylation microarrays.
getRed Class '"RGChannelSet"'
getUnmeth Class MethylSet
IlluminaMethylationAnnotation-class Class '"IlluminaMethylationAnnotation"'
IlluminaMethylationManifest-class Class '"IlluminaMethylationManifest"'
ilogit2 logit in base 2.
initialize-method Class MethylSet
initialize-method Class '"RGChannelSet"'
logit2 logit in base 2.
manifestNew Class '"IlluminaMethylationManifest"'
mdsPlot Multi-dimensional scaling plots giving an overview of similarities and differences between samples.
MethylSet Class MethylSet
MethylSet-class Class MethylSet
minfi Analyze Illumina's methylation arrays
normalize.illumina.control Perform preprocessing as Genome Studio.
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.
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"'
show-method Class '"IlluminaMethylationAnnotation"'
show-method Class '"IlluminaMethylationManifest"'
show-method Class MethylSet
show-method Class '"RGChannelSet"'