| .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
|
