API for hansenlab/minfi
Analyze Illumina Infinium DNA methylation arrays

Global functions
.NA_type Source code
.annoGet Source code
.availableAnnotation Source code
.betaFromMethUnmeth Source code
.buildControlMatrix450k Source code
.checkAssayNames Source code
.checkSex Source code
.convertArray_450k_epic Source code
.digestMatrix Source code
.digestVector Source code
.doSnpOverlap Source code
.extractFromRGSet450k Source code
.extractOpenClosed Source code
.fixMethOutliers Source code
.fsvd Source code
.getAddressesNotInManifest Source code
.getAnnotationFromOutType Source code
.getAnnotationString Source code
.getFirstPC Source code
.getFunnormIndices Source code
.getIslandAnnotation Source code
.getLociFromOutType Source code
.getManifestString Source code
.getProbePositionsDetailed Source code
.getSex Source code
.guessArrayTypes Source code
.harmonizeDataFrames Source code
.harmonizeSex Source code
.highestType Source code
.imputeMatrix Source code
.is27k Source code
.is450k Source code
.isDelayedArrayBacked Source code
.isEPIC Source code
.isGenomicOrStop Source code
.isMatrixBacked Source code
.isMatrixBackedOrStop Source code
.isMatrixBackedOrWarning Source code
.isMethylOrRatio Source code
.isMethylOrStop Source code
.isRGOrStop Source code
.meanSmoother Source code
.normalizeFunnorm450k Source code
.normalizeMatrix Source code
.pDataAdd Source code
.pDataFix Source code
.qnormNotStratified Source code
.qnormStratified Source code
.qnormStratifiedHelper Source code
.regularizeQuantiles Source code
.removeBadBins Source code
.returnBinnedMatrix Source code
.returnFit Source code
.returnFitBySex Source code
.show.annotation Source code
.show.availableAnnotation Source code
.show.preprocessMethod Source code
.unitarize Source code
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
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
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
aveQuantile 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
bumphunter,GenomicRatioSet-method Man page
clusterMaker4Blocks Source code
coerce,RGChannelSetExtended,RGChannelSet-method Man page
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
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
dimnames,arrayRealizationSink-method Man page
dmpFinder Man page 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
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
gaphunter Man page Source code
getAnnotation Man page Source code
getAnnotationObject Man page 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
getGenomicRatioSetFromGEO Man page Source code
getGreen Man page Source code
getIslandStatus Man page Source code
getLocations Man page 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
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
getProbeType Man page Source code
getQC Man page Source code
getRed Man page Source code
getSex Man page 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
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
minfi Man page
minfi-defunct Man page
minfi-deprecated Man page
minfi-package Man page
minfiQC Man page Source code
normaliseChannel Source code
normalize.illumina.control Man page 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
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
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.manifest.Mammal Source code
read.metharray Man page Source code
read.metharray.exp Man page Source code
read.metharray.sheet Man page Source code
read.metharray2 Source code
readGEORawFile Man page Source code
readTCGA Man page 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
subsetByLoci Man page Source code
subsetQuantileNorm Source code
type,HDF5RealizationSink-method Man page
type,RleRealizationSink-method Man page
type,arrayRealizationSink-method Man page
validationCellType Source code
hansenlab/minfi documentation built on March 7, 2020, 10:12 p.m.