BetaValueToMValue       Convert beta-value to M-value
DML                     Test differential methylation on each locus
DMLShrinkage            Test differential methylation on each locus
                        Using Shrinkage Estimator
DMR                     Find Differentially Methylated Region (DMR)
IG                      IG getter generic
IG<-                    IG replacement generic
IGpass                  Get IG slot of SigSet class that passes mask
                        This is the same as IG() if there is no mask
                        set
II                      II getter generic
II<-                    II replacement generic
IIpass                  Get II slot of SigSet class that passes mask
                        This is the same as II() if there is no mask
                        set
IR                      IR getter generic
IR<-                    IR replacement generic
IRpass                  Get IR slot of SigSet class that passes mask
                        This is the same as IR() if there is no mask
                        set
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
addMask                 Add probes to mask
as.data.frame.sesameQC
                        Coerce a sesameQC into a dataframe
bSubComplete            subset beta value matrix by complete probes
bSubMostVariable        Get most variable probes
bSubProbes              subset beta value matrix by probes
betaToAF                convert betas to variant allele frequency
binSignals              Bin signals from probe signals
bisConversionControl    Compute internal bisulfite conversion control
buildControlMatrix450k
                        Build control summary matrix
checkLevels             filter data matrix by factor completeness
chipAddressToSignal     Lookup address in one sample
cnSegmentation          Perform copy number segmentation
compareMouseBloodReference
                        Compare beta value against mouse blood
                        reference
compareMouseTissueReference
                        Compare mouse array data with mouse tissue
                        references
createUCSCtrack         Turn beta values into a UCSC browser track
ctl                     ctl getter generic
ctl<-                   ctl replacement generic
deIdentify              De-identify IDATs by removing SNP probes
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
detectionPoobEcdf2      Detection P-value based on ECDF of out-of-band
                        signal
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
extra                   extra getter generic
extra<-                 extra replacement generic
extractDesign           Extract the first design category
formatVCF               Convert SNP from Infinium array to VCF file
getAFTypeIbySumAlleles
                        Get allele frequency treating type I by summing
                        alleles
getAutosomeProbes       Get autosome probes
getBetas                Get beta Values
getBinCoordinates       Get bin coordinates
getNormCtls             get normalization control signal
getProbesByChromosome   Get Probes by Chromosome
getProbesByGene         Get Probes by Gene
getProbesByRegion       Get probes by genomic region
getProbesByTSS          Get Probes by Gene Transcription Start Site
                        (TSS)
getRefSet               Retrieve reference set
getSexInfo              Get sex-related information
inferEthnicity          Infer Ethnicity
inferSex                Infer Sex
inferSexKaryotypes      Infer Sex Karyotype
inferStrain             Infer strain information for mouse array
inferTypeIChannel       Infer and reset color channel for Type-I probes
                        instead of using what is specified in manifest.
                        The results are stored to sset@extra$IGG and
                        sset@extra$IRR slot.
initFileSet             initialize a fileSet class by allocating
                        appropriate storage
isUniqProbeID           Whether the probe ID is the uniq probe ID like
                        in the mouse array, e.g., cg36609548
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)
mask                    Get current mask of SigSet class
meanIntensity           Mean Intensity
noob                    Noob background correction
noobsb                  Background subtraction with bleeding-through
                        subtraction
oobG                    oobG getter generic
oobG<-                  oobG replacement generic
oobGpass                Get oobG slot of SigSet class that passes mask
                        This is the same as oobG() if there is no mask
                        set
oobR                    oobR getter generic
oobR<-                  oobR replacement generic
oobRpass                Get oobR slot of SigSet class that passes mask
                        This is the same as oobR() if there is no mask
                        set
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
predictMouseAgeInMonth
                        Mouse age predictor
print.DMLSummary        Print DMLSummary object
print.fileSet           Print a fileSet
print.sesameQC          Print sesameQC object
probeID_designType      Extract the probe type field from probe ID This
                        only works with the new probe ID system. See
                        https://github.com/zhou-lab/InfiniumAnnotation
                        for illustration
probeNames              Get Probe Names of SigSet class
pval                    pval getter generic
pval<-                  pval replacement generic
qualityMask             Mask beta values by design quality
qualityRank             This function looks at public data of similar
                        nature e.g., tissue, FFPE vs non-FFPE, etc to
                        evaluate the quality of the target data quality
reIdentify              Re-identify IDATs by restoring scrambled SNP
                        intensities
readFileSet             Read an existing fileSet from storage
readIDATpair            Import a pair of IDATs from one sample
reopenSesame            re-compute beta value for GenomicRatioSet
resetMask               Reset Masking
restoreMask             Save current mask
saveMask                Save current mask
scrub                   SCRUB background correction
scrubSoft               SCRUB background correction
searchIDATprefixes      Identify IDATs from a directory
segmentBins             Segment bins using DNAcopy
sesame-package          Analyze DNA methylation data
sesamePlotIntensVsBetas
                        Plot Total Signal Intensities vs Beta Values
                        This plot is helpful in revealing the extent of
                        signal background and dye bias.
sesamePlotRedGrnQQ      Plot red-green QQ-Plot using Infinium-I Probes
sesameQC                Generate summary numbers that indicative of
                        experiment quality Please provide a raw sigset
                        (before any preprocessing). Usually directly
                        from readIDATpair
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
setMask                 Set mask to only the probes specified
show,SigSet-method      The display method for SigSet
signalMU                report M and U for regular probes
sliceFileSet            Slice a fileSet with samples and probes
subsetSignal            Select a subset of probes
summaryExtractCfList    Extract Coefficient Table List from DMLSummary
                        This function returns a list of coefficients
                        for each variable tested.
summaryExtractTest      Extract slope information from DMLSummary
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
