addMask                 Add probes to mask
assemble_plots          assemble plots
betasCollapseToPfx      Collapse betas by averagng probes with common
                        probe ID prefix
BetaValueToMValue       Convert beta-value to M-value
binSignals              Bin signals from probe signals
bisConversionControl    Compute internal bisulfite conversion control
calcEffectSize          Compute effect size for different variables
                        from prediction matrix
checkLevels             filter data matrix by factor completeness only
                        works for discrete factors
chipAddressToSignal     Lookup address in one sample
cnSegmentation          Perform copy number segmentation
compareMouseStrainReference
                        Compare Strain SNPs with a reference panel
compareReference        Compare array data with references (e.g.,
                        tissue, cell types)
controls                get the controls attributes
convertProbeID          Convert Probe ID
createUCSCtrack         Turn beta values into a UCSC browser track
dataFrame2sesameQC      Convert data frame to sesameQC object
deIdentify              De-identify IDATs by removing SNP probes
detectionPnegEcdf       Detection P-value based on ECDF of negative
                        control
diffRefSet              Restrict refset to differentially methylated
                        probes use with care, might introduce bias
dmContrasts             List all contrasts of a DMLSummary
DML                     Test differential methylation on each locus
DMLpredict              Predict new data from DML
DMR                     Find Differentially Methylated Region (DMR)
dyeBiasCorr             Correct dye bias in by linear scaling.
dyeBiasCorrMostBalanced
                        Correct dye bias using most balanced sample as
                        the reference
dyeBiasL                Correct dye bias in by linear scaling.
dyeBiasNL               Dye bias correction by matching green and red
                        to mid point
ELBAR                   ELiminate BAckground-dominated Reading (ELBAR)
estimateLeukocyte       Estimate leukocyte fraction using a
                        two-component model
formatVCF               Convert SNP from Infinium array to VCF file
getAFs                  Get allele frequency
getAFTypeIbySumAlleles
                        Get allele frequency treating type I by summing
                        alleles
getBetas                Get beta Values
getBinCoordinates       Get bin coordinates
getMask                 get probe masking by mask names
getRefSet               Retrieve reference set
imputeBetas             Impute of missing data of specific platform
imputeBetasByGenomicNeighbors
                        Impute missing data based on genomic neighbors.
imputeBetasMatrixByMean
                        Impute Missing Values with Mean This function
                        replaces missing values (NA) in a matrix,
                        default is row means.
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.
inferSpecies            Infer Species
inferStrain             Infer strain information for mouse array
inferTissue             inferTissue 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
listAvailableMasks      list existing quality masks for a SigDF
mapFileSet              Deposit data of one sample to a fileSet (and
                        hence to file)
mapToMammal40           Map the SDF (from overlap array platforms)
                        Replicates are merged by picking the best
                        detection
matchDesign             normalize Infinium I probe betas to Infinium II
meanIntensity           Whole-dataset-wide Mean Intensity
medianTotalIntensity    Whole-dataset-wide Median Total Intensity (M+U)
mLiftOver               Lift over beta values or SigDFs to another
                        Infinium platform This function wraps ID
                        conversion and provide optional imputation
                        functionality.
MValueToBetaValue       Convert M-value to beta-value
negControls             get negative control signal
noMasked                remove masked probes from SigDF
noob                    Noob background subtraction
normControls            get normalization control signal
openSesame              The openSesame pipeline
openSesameToFile        openSesame pipeline with file-backed storage
palgen                  Generate some additional color palettes
parseGEOsignalMU        Convert signal M and U to SigDF
pOOBAH                  Detection P-value based on ECDF of out-of-band
                        signal
predictAge              Predict age using linear models
prefixMask              Mask SigDF by probe ID prefix
prefixMaskButC          Mask all but C probes in SigDF
prefixMaskButCG         Mask all but CG probes in SigDF
prepSesame              Apply a chain of sesame preprocessing functions
                        in an arbitrary order
prepSesameList          List supported prepSesame functions
print.DMLSummary        Print DMLSummary object
print.fileSet           Print a fileSet
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
readFileSet             Read an existing fileSet from storage
readIDATpair            Import a pair of IDATs from one sample
recommendedMaskNames    Recommended mask names for each Infinium
                        platform
reIdentify              Re-identify IDATs by restoring scrambled SNP
                        intensities
resetMask               Reset Masking
scrub                   SCRUB background correction
scrubSoft               SCRUB background correction
sdf_read_table          read a table file to SigDF
sdf_write_table         write SigDF to table file
SDFcollapseToPfx        collapse to probe prefix
sdfPlatform             Convenience function to output platform
                        attribute of SigDF
searchIDATprefixes      Identify IDATs from a directory
segmentBins             Segment bins using DNAcopy
sesame_checkVersion     Check SeSAMe versions
sesame-package          Analyze DNA methylation data
sesameAnno_attachManifest
                        Annotate a data.frame using manifest
sesameAnno_buildAddressFile
                        Build sesame ordering address file from tsv
sesameAnno_buildManifestGRanges
                        Build manifest GRanges from tsv
sesameAnno_download     Download SeSAMe annotation files
sesameAnno_readManifestTSV
                        Read manifest file to a tsv format
sesameQC_calcStats      Calculate QC statistics
sesameQC_getStats       Get stat numbers from an sesameQC object
sesameQC_plotBar        Bar plots for sesameQC
sesameQC_plotBetaByDesign
                        Plot betas distinguishing different Infinium
                        chemistries
sesameQC_plotHeatSNPs   Plot SNP heatmap
sesameQC_plotIntensVsBetas
                        Plot Total Signal Intensities vs Beta Values
                        This plot is helpful in revealing the extent of
                        signal background and dye bias.
sesameQC_plotRedGrnQQ   Plot red-green QQ-Plot using Infinium-I Probes
sesameQC_rankStats      This function compares the input sample with
                        public data. Only overlapping metrics will be
                        compared.
sesameQC-class          An S4 class to hold QC statistics
sesameQCtoDF            Convert a list of sesameQC to data frame
setMask                 Set mask to only the probes specified
SigDF                   SigDF validation from a plain data frame
signalMU                report M and U for regular probes
sliceFileSet            Slice a fileSet with samples and probes
summaryExtractTest      Extract slope information from DMLSummary
totalIntensities        M+U Intensities Array
twoCompsEst2            Estimate the fraction of the 2nd component in a
                        2-component mixture
updateSigDF             Set color and mask using
                        strain/species-specific manifest
visualizeGene           Visualize Gene
visualizeProbes         Visualize Region that Contains the Specified
                        Probes
visualizeRegion         Visualize Region
visualizeSegments       Visualize segments
