API for minfi
Analyze Illumina Infinium DNA methylation arrays

Global functions
GenomicMethylSet Man page Source code
GenomicMethylSet-class Man page
GenomicRatioSet Man page Source code
GenomicRatioSet-class Man page
IlluminaMethylationAnnotation Man page Source code
IlluminaMethylationAnnotation-class Man page
IlluminaMethylationManifest Man page Source code
IlluminaMethylationManifest-class Man page
MethylSet Man page Source code
MethylSet-class Man page
NA_type Source code
RGChannelSet Man page Source code
RGChannelSet-class Man page
RGChannelSetExtended Man page Source code
RGChannelSetExtended-class Man page
RatioSet Man page Source code
RatioSet-class Man page
addQC Man page Source code
addSex Man page Source code
addSnpInfo Man page Source code
annoGet Source code
annotation,GenomicMethylSet-method Man page
annotation,GenomicRatioSet-method Man page
annotation,MethylSet-method Man page
annotation,RGChannelSet-method Man page
annotation,RatioSet-method Man page
annotation<-,GenomicMethylSet,ANY-method Man page
annotation<-,GenomicRatioSet,ANY-method Man page
annotation<-,MethylSet,ANY-method Man page
annotation<-,RGChannelSet,ANY-method Man page
annotation<-,RatioSet,ANY-method Man page
availableAnnotation Source code
aveQuantile Source code
betaFromMethUnmeth Source code
bgIntensitySwan Source code
bgcorrect.illumina Man page Source code
blockApplyWithRealization Source code
blockFinder Man page Source code
blockMapply Source code
blockMapplyWithRealization Source code
buildControlMatrix450k Source code
bumphunter,GenomicRatioSet-method Man page
checkAssayNames Source code
checkSex Source code
clusterMaker4Blocks Source code
coerce,RGChannelSetExtended,RGChannelSet-method Man page
colGrid Source code
combine,GenomicMethylSet,GenomicMethylSet-method Man page
combine,GenomicRatioSet,GenomicRatioSet-method Man page
combine,MethylSet,MethylSet-method Man page
combine,RGChannelSet,RGChannelSet-method Man page
combine,RatioSet,RatioSet-method Man page
combineArrays Man page
combineArrays,GenomicMethylSet,GenomicMethylSet-method Man page
combineArrays,GenomicRatioSet,GenomicRatioSet-method Man page
combineArrays,MethylSet,MethylSet-method Man page
combineArrays,RGChannelSet,RGChannelSet-method Man page
combineArrays,RatioSet,RatioSet-method Man page
compartments Man page Source code
controlStripPlot Man page Source code
convertArray Man page
convertArray,GenomicMethylSet-method Man page
convertArray,GenomicRatioSet-method Man page
convertArray,MethylSet-method Man page
convertArray,RGChannelSet-method Man page
convertArray,RatioSet-method Man page
convertArray_450k_epic Source code
cpgCollapse Man page Source code
cpgCollapseAnnotation Source code
createCorMatrix Man page Source code
densityBeanPlot Man page Source code
densityPlot Man page Source code
detectionP Man page Source code
digestMatrix Source code
digestVector Source code
dimnames,arrayRealizationSink-method Man page
dmpFinder Man page Source code
doSnpOverlap Source code
dropLociWithSnps Man page Source code
dropMethylationLoci Man page Source code
dyeCorrection Source code
estimateCellCounts Man page Source code
extractAB Man page Source code
extractFromRGSet450k Source code
extractOpenClosed Source code
featureNames,GenomicMethylSet-method Man page
featureNames,GenomicRatioSet-method Man page
featureNames,MethylSet-method Man page
featureNames,RGChannelSet-method Man page
featureNames,RatioSet-method Man page
featureNames<-,GenomicMethylSet-method Man page
featureNames<-,GenomicRatioSet-method Man page
featureNames<-,MethylSet-method Man page
featureNames<-,RGChannelSet-method Man page
featureNames<-,RatioSet-method Man page
fixMethOutliers Man page Source code Source code
fsvd Source code
gaphunter Man page Source code
getAddressesNotInManifest Source code
getAnnotation Man page Source code
getAnnotationFromOutType Source code
getAnnotationObject Man page Source code
getAnnotationString Source code
getBeta Man page
getBeta,GenomicMethylSet-method Man page
getBeta,GenomicRatioSet-method Man page
getBeta,MethylSet-method Man page
getBeta,RGChannelSet-method Man page
getBeta,RatioSet-method Man page
getCN Man page
getCN,GenomicMethylSet-method Man page
getCN,GenomicRatioSet-method Man page
getCN,MethylSet-method Man page
getCN,RatioSet-method Man page
getControlAddress Man page Source code
getFirstPC Source code
getFunnormIndices Source code
getGenomicRatioSetFromGEO Man page Source code
getGreen Man page Source code
getIslandAnnotation Source code
getIslandStatus Man page Source code
getLocations Man page Source code
getLociFromOutType Source code
getM Man page
getM,GenomicMethylSet-method Man page
getM,GenomicRatioSet-method Man page
getM,MethylSet-method Man page
getM,RatioSet-method Man page
getManifest Man page
getManifest,IlluminaMethylationAnnotation-method Man page
getManifest,IlluminaMethylationManifest-method Man page
getManifest,MethylSet-method Man page
getManifest,RGChannelSet-method Man page
getManifest,character-method Man page
getManifestInfo Man page Source code
getManifestString Source code
getMeth Man page
getMeth,GenomicMethylSet-method Man page
getMeth,MethylSet-method Man page
getMethSignal Man page Source code
getNBeads Man page Source code
getOOB Man page Source code
getProbeInfo Man page Source code
getProbePositionsDetailed Source code
getProbeType Man page Source code
getQC Man page Source code
getRed Man page Source code
getSex Man page Source code Source code
getSnpBeta Man page Source code
getSnpInfo Man page Source code
getSubset Source code
getUnmeth Man page
getUnmeth,GenomicMethylSet-method Man page
getUnmeth,MethylSet-method Man page
guessArrayTypes Source code
harmonizeDataFrames Source code
harmonizeSex Source code
highestType Source code
ilogit2 Man page Source code
logit2 Man page Source code
makeGenomicRatioSetFromMatrix Man page Source code
mapToGenome Man page
mapToGenome,GenomicMethylSet-method Man page
mapToGenome,GenomicRatioSet-method Man page
mapToGenome,MethylSet-method Man page
mapToGenome,RGChannelSet-method Man page
mapToGenome,RatioSet-method Man page
mapToGenome-methods Man page
mdsPlot Man page Source code
meanSmoother Source code
minfi Man page
minfi-defunct Man page
minfi-deprecated Man page
minfi-package Man page
minfiQC Man page Source code
mputeMatrix Source code
normaliseChannel Source code
normalize.illumina.control Man page Source code
normalizeFunnorm450k Source code
normalizeMatrix Source code
normexp.get.xcs Source code
normexp.get.xs Source code
pData,GenomicMethylSet-method Man page
pData,GenomicRatioSet-method Man page
pData,MethylSet-method Man page
pData,RGChannelSet-method Man page
pData,RatioSet-method Man page
pData<-,GenomicMethylSet,DataFrame-method Man page
pData<-,GenomicRatioSet,DataFrame-method Man page
pData<-,MethylSet,DataFrame-method Man page
pData<-,RGChannelSet,DataFrame-method Man page
pData<-,RatioSet,DataFrame-method Man page
pDataAdd Source code
pDataFix Source code
pickCompProbes Source code
plotBetasByType Man page Source code
plotCpg Man page Source code
plotQC Man page Source code
plotSex Man page Source code
preprocessFunnorm Man page Source code
preprocessIllumina Man page Source code
preprocessMethod Man page
preprocessMethod,GenomicMethylSet-method Man page
preprocessMethod,GenomicRatioSet-method Man page
preprocessMethod,MethylSet-method Man page
preprocessMethod,RatioSet-method Man page
preprocessNoob Man page Source code
preprocessQuantile Man page Source code
preprocessRaw Man page Source code
preprocessSWAN Man page Source code
projectCellType Source code
qcReport Man page Source code
qnormNotStratified Source code
qnormStratified Source code
qnormStratifiedHelper Source code
ratioConvert Man page
ratioConvert,GenomicMethylSet-method Man page
ratioConvert,MethylSet-method Man page
ratioConvert-methods Man page
read.450k Man page Source code
read.450k.exp Man page Source code
read.450k.sheet Man page Source code
read.GenomeStudio Source code
read.manifest.27k Source code
read.manifest.450k Source code
read.manifest.EPIC Source code
read.metharray Man page Source code
read.metharray.exp Man page Source code
read.metharray.sheet Man page Source code
readGEORawFile Man page Source code
readTCGA Man page Source code
regularizeQuantiles Source code
removeBadBins Source code
returnBinnedMatrix Source code
returnFit Source code
returnFitBySex Source code
rowGrid Source code
s27k Source code
s450k Source code
sDelayedArrayBacked Source code
sEPIC Source code
sGenomicOrStop Source code
sMatrixBacked Source code
sMatrixBackedOrStop Source code
sMatrixBackedOrWarning Source code
sMethylOrRatio Source code
sMethylOrStop Source code
sRGOrStop Source code
sampleNames,GenomicMethylSet-method Man page
sampleNames,GenomicRatioSet-method Man page
sampleNames,MethylSet-method Man page
sampleNames,RGChannelSet-method Man page
sampleNames,RatioSet-method Man page
sampleNames<-,GenomicMethylSet,ANY-method Man page
sampleNames<-,GenomicRatioSet,ANY-method Man page
sampleNames<-,MethylSet,ANY-method Man page
sampleNames<-,RGChannelSet,ANY-method Man page
sampleNames<-,RatioSet,ANY-method Man page
show,GenomicMethylSet-method Man page
show,GenomicRatioSet-method Man page
show,IlluminaMethylationAnnotation-method Man page
show,IlluminaMethylationManifest-method Man page
show,MethylSet-method Man page
show,RGChannelSet-method Man page
show,RatioSet-method Man page
show.annotation Source code
show.availableAnnotation Source code
show.preprocessMethod Source code
subsetByLoci Man page Source code
subsetQuantileNorm Source code
type,HDF5RealizationSink-method Man page
type,RleRealizationSink-method Man page
type,arrayRealizationSink-method Man page
unitarize Source code
validationCellType Source code
minfi documentation built on June 17, 2018, 6 p.m.