BetaValueToMValue       Convert beta-value to M-value
DML                     Test differential methylation on each locus
DMR                     Find Differentially Methylated Region (DMR)
IG                      IG getter generic
IG<-                    IG replacement generic
II                      II getter generic
II<-                    II replacement generic
IR                      IR getter generic
IR<-                    IR replacement generic
MValueToBetaValue       Convert M-value to beta-value
RGChannelSetToSigSets   Convert RGChannelSet (minfi) to a list of
                        SigSet (SeSAMe)
SNPcheck                Check sample identity using SNP probes
SigSet-class            SigSet class
SigSetList              constructor
SigSetList-class        a List of SigSets with some methods of its own
SigSetList-methods      SigSetList methods (centralized).  Currently
                        scarce... 'show' print a summary of the
                        SigSetList.
SigSetListFromIDATs     read IDATs into a SigSetList
SigSetListFromPath      read an entire directory's worth of IDATs into
                        a SigSetList
SigSetToRatioSet        Convert one sesame::SigSet to minfi::RatioSet
SigSetsToRGChannelSet   Convert sesame::SigSet to minfi::RGChannelSet
as.data.frame.sesameQC
                        Coerce a sesameQC into a dataframe
binSignals              Bin signals from probe signals
bisConversionControl    Compute internal bisulfite conversion control
buildControlMatrix450k
                        Build control summary matrix
chipAddressToSignal     Lookup address in one sample
cnSegmentation          Perform copy number segmentation
ctl                     ctl getter generic
ctl<-                   ctl replacement generic
detectionPfixedNorm     Detection P-value based on normal fitting with
                        gived parameters
detectionPnegEcdf       Detection P-value based on ECDF of negative
                        control
detectionPnegNorm       Detection P-value based on normal fitting the
                        negative controls
detectionPnegNormGS     Detection P-value emulating Genome Studio
detectionPnegNormTotal
                        Detection P-value based on normal fitting the
                        negative controls, channels are first summed
detectionPoobEcdf       Detection P-value based on ECDF of out-of-band
                        signal
detectionZero           Detection P-value set to all zero
diffRefSet              Restrict refset to differentially methylated
                        probes use with care, might introduce bias
dyeBiasCorr             Correct dye bias in by linear scaling.
dyeBiasCorrMostBalanced
                        Correct dye bias using most balanced sample as
                        the reference
dyeBiasCorrTypeINorm    Dye bias correction by matching green and red
                        to mid point
estimateCellComposition
                        Estimate cell composition using reference
estimateLeukocyte       Estimate leukocyte fraction using a
                        two-component model
getAFTypeIbySumAlleles
                        Get allele frequency treating type I by summing
                        alleles
getBetas                Get beta Values
getBinCoordinates       Get bin coordinates
getNormCtls             get normalization control signal
getProbesByGene         Get Probes by Gene
getProbesByRegion       Get probes by genomic region
getProbesByTSS          Get Probes by Gene Transcription Start Site
                        (TSS)
getRefSet               Retrieve reference set
getSegment              Select segment from coefficient table
getSexInfo              Get sex-related information
inferEthnicity          Infer Ethnicity
inferSex                Infer Sex
inferSexKaryotypes      Infer Sex Karyotype
inferTypeIChannel       Infer and reset color channel for Type-I probes
                        instead of using what is specified in manifest
initFileSet             initialize a fileSet class by allocating
                        appropriate storage
makeExampleSeSAMeDataSet
                        Make a simulated SeSAMe data set
makeExampleTinyEPICDataSet
                        Make a tiny toy simulated EPIC data set
mapFileSet              Deposit data of one sample to a fileSet (and
                        hence to file)
meanIntensity           Mean Intensity
noob                    Noob background correction
noobsb                  Background subtraction with bleeding-through
                        subtraction
oobG                    oobG getter generic
oobG<-                  oobG replacement generic
oobR                    oobR getter generic
oobR<-                  oobR replacement generic
openSesame              The openSesame pipeline
openSesameToFile        openSesame pipeline with file-backed storage
parseGEOSignalABFile    Parse GEO signal-A/B File into a SigSet List
predictAgeHorvath353    Horvath 353 age predictor
predictAgePheno         Phenotypic age predictor
predictAgeSkinBlood     Horvath Skin and Blood age predictor
print.fileSet           Print a fileSet
print.sesameQC          Print sesameQC object
probeNames              Get Probe Names of SigSet class
pval                    pval getter generic
pval<-                  pval replacement generic
readFileSet             Read an existing fileSet from storage
readIDATpair            Import a pair of IDATs from one sample
reopenSesame            re-compute beta value for GenomicRatioSet
searchIDATprefixes      Identify IDATs from a directory
segmentBins             Segment bins using DNAcopy
sesame-package          Analyze DNA methylation data
sesameQC                Generate summary numbers that indicative of
                        experiment quality
sesamize                "fix" an RGChannelSet (for which IDATs may be
                        unavailable) with Sesame The input is an RGSet
                        and the output is a sesamized
                        minfi::GenomicRatioSet
show,SigSet-method      The display method for SigSet
sliceFileSet            Slice a fileSet with samples and probes
subsetSignal            Select a subset of probes
topLoci                 Top loci in differential methylation
topSegments             Top segments in differential methylation
totalIntensities        M+U Intensities for All Probes
totalIntensityZscore    Calculate intensity Z-score
twoCompsEst2            Estimate the fraction of the 2nd component in a
                        2-component mixture
visualizeGene           Visualize Gene
visualizeProbes         Visualize Region that Contains the Specified
                        Probes
visualizeRegion         Visualize Region
visualizeSegments       Visualize segments
