BetaValueToMValue       Convert beta-value to M-value
DML                     Test differential methylation on each locus
DMR                     Find Differentially Methylated Region (DMR)
MValueToBetaValue       Convert M-value to beta-value
RGChannelSetToSigDFs    Convert RGChannelSet (minfi) to a list of SigDF
                        (SeSAMe)
SNPcheck                Check sample identity using SNP probes
SigDF                   SigDF constructor from a plain data frame
SigDFToRatioSet         Convert one sesame::SigDF to minfi::RatioSet
SigDFsToRGChannelSet    Convert sesame::SigDF to minfi::RGChannelSet
addMask                 Add probes to mask
as.data.frame.sesameQC
                        Coerce a sesameQC into a dataframe
attachManifest          Annotate a data.frame using manifest
bSubComplete            subset beta value matrix by complete probes
bSubMostVariable        Get most variable probes
bSubProbes              subset beta value matrix by probes
binSignals              Bin signals from probe signals
bisConversionControl    Compute internal bisulfite conversion control
calcDatabaseSetStatistics1
                        calcDatabaseSetStatistics1 calculates features
                        of x
calcDatabaseSetStatisticsAll
                        calcDatabaseSetStatisticsAll builds dataset for
                        a given betas matrix composed of engineered
                        features from the given database sets
checkLevels             filter data matrix by factor completeness only
                        works for discrete factors
chipAddressToSignal     Lookup address in one sample
cnSegmentation          Perform copy number segmentation
compareDatbaseSetOverlap
                        compareDatbaseSetOverlap calculates the
                        pariwise overlap between given list of database
                        sets using a distance metric.
compareMouseStrainReference
                        Compare Strain SNPs with a reference panel
compareMouseTissueReference
                        Compare mouse array data with mouse tissue
                        references
controls                get the controls attributes
createDatabaseSetNetwork
                        createGeneNetwork creates databaseSet network
                        using the Jaccard index.
createUCSCtrack         Turn beta values into a UCSC browser track
deIdentify              De-identify IDATs by removing SNP probes
detectionPnegEcdf       Detection P-value based on ECDF of negative
                        control
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
dmContrasts             List all contrasts of a DMLSummary
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
dyeBiasDistortion       Quantify how much dye bias in high signal range
                        deviates from the global median
estimateCellComposition
                        Estimate cell composition using reference
estimateLeukocyte       Estimate leukocyte fraction using a
                        two-component model
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
getDatabaseSetOverlap   getDatabaseSetOverlap tests for the overlap of
                        set of probes (querySet) in a single given
                        feature (database set)
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
inferInfiniumIChannel   Infer and reset color channel for Type-I probes
                        instead of using what is specified in manifest.
                        The results are stored to sdf@extra$IGG and
                        sdf@extra$IRR slot.
inferSex                Infer Sex
inferSexKaryotypes      Infer Sex Karyotype
inferSpecies            Infer Species
inferStrain             Infer strain information for mouse array
inferTissue             inferTissue1 infers the tissue of a single
                        sample (as identified through the branchIDs in
                        the row data of the reference) by reporting
                        independent composition through cell type
                        deconvolution.
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
mapFileSet              Deposit data of one sample to a fileSet (and
                        hence to file)
meanIntensity           Whole-dataset-wide Mean Intensity
medianTotalIntensity    Whole-dataset-wide Median Total Intensity (M+U)
neob                    Negative control plus out-of-band background
                        correction
noMasked                remove masked probes from SigDF
noob                    Noob background correction
openSesame              The openSesame pipeline
openSesameToFile        openSesame pipeline with file-backed storage
plotLollipop            plotLollipop creates a lollipop plot of
                        log(estimate) given data with fields estimate.
plotVolcano             plotVolcano creates a volcano plot of
                        -log2(p.value) and log(estimate) given data
                        with fields estimate and p.value.
predictAgeHorvath353    Horvath 353 age predictor
predictAgeSkinBlood     Horvath Skin and Blood age predictor
predictMouseAgeInMonth
                        Mouse age predictor
print.DMLSummary        Print DMLSummary object
print.SigDF             Print SigDF 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
probeSuccessRate        Whole-dataset-wide Probe Success Rate
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
scrub                   SCRUB background correction
scrubSoft               SCRUB background correction
sdfPlatform             Convenience function to output platform
                        attribute of SigDF
sdf_read_table          read a table file to SigDF
sdf_write_table         write SigDF to table file
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
                        SigDF(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
setMaskBySpecies        Set mask using species-specific manifest
signalMU                report M and U for regular probes
sliceFileSet            Slice a fileSet with samples and probes
summaryExtractTest      Extract slope information from DMLSummary
testEnrichment          testEnrichment tests for the enrichment of set
                        of probes (query set) in a number of features
                        (database sets).
testEnrichment1         testEnrichment1 tests for the enrichment of set
                        of probes (query set) in a single given feature
                        (database set)
testEnrichmentFGSEA     testEnrichmentFGSEA uses the FGSEA test to
                        estimate the association of a categorical
                        variable against a continuous variable.
testEnrichmentFisher    testEnrichmentFisher uses Fisher's exact test
                        to estimate the association between two
                        categorical variables.
testEnrichmentGene      testEnrichmentGene tests for the enrichment of
                        set of probes (querySet) in gene regions.
testEnrichmentSpearman
                        testEnrichmentSpearman uses the Spearman
                        statistical test to estimate the association
                        between two continuous variables.
totalIntensities        M+U Intensities Array
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
