Package: sesame 1.31.0

Wanding Zhou

sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Tools For analyzing Illumina Infinium DNA methylation arrays. SeSAMe provides utilities to support analyses of multiple generations of Infinium DNA methylation BeadChips, including preprocessing, quality control, visualization and inference. SeSAMe features accurate detection calling, intelligent inference of ethnicity, sex and advanced quality control routines.

Authors:Wanding Zhou [aut, cre, fnd], Wubin Ding [ctb], David Goldberg [ctb], Ethan Moyer [ctb], Bret Barnes [ctb], Timothy Triche [ctb], Hui Shen [aut, fnd]

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manual.pdf |manual.html✨
card.svg |card.png
sesame/json (API)
NEWS

# Install 'sesame' in R:
install.packages('sesame', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zwdzwd/sesame/issues

On BioConductor:sesame-1.31.0(bioc 3.24)sesame-1.30.0(bioc 3.23)

dnamethylationmethylationarraypreprocessingqualitycontrolbioinformaticsdna-methylationmicroarray

10.62 score 82 stars 1 packages 350 scripts 1.5k downloads 2 mentions 101 exports 99 dependencies

Last updated from:9dcdf06137. Checks:1 NOTE, 9 OK. Indexed: yes.

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windows-develOK752
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wasm-releaseOK167

Exports:addMaskbetasCollapseToPfxBetaValueToMValuebisConversionControlcalcEffectSizecheckLevelscnSegmentationcompareMouseStrainReferencecompareReferencecontrolscreateUCSCtrackdeIdentifydetectionPnegEcdfdiffRefSetdmContrastsDMLDMLpredictDMRdyeBiasCorrdyeBiasCorrMostBalanceddyeBiasCorrTypeINormdyeBiasLdyeBiasNLELBARestimateLeukocyteformatVCFgetAFsgetAFTypeIbySumAllelesgetBetasgetMaskgetRefSetimputeBetasimputeBetasByGenomicNeighborsimputeBetasMatrixByMeaninferInfiniumIChannelinferSexinferSpeciesinferStraininferTissueinitFileSetlistAvailableMasksmapFileSetmapToMammal40matchDesignmeanIntensitymedianTotalIntensitymLiftOverMValueToBetaValuenoMaskednoobopenSesameopenSesameToFilepalgenparseGEOsignalMUpOOBAHpredictAgeprefixMaskprefixMaskButCprefixMaskButCGprepSesameprepSesameListprobeID_designTypeprobeSuccessRatequalityMaskreadFileSetreadIDATpairrecommendedMaskNamesreIdentifyresetMaskscrubscrubSoftsdf_read_tablesdf_write_tablesdfPlatformsearchIDATprefixessesame_checkVersionsesameAnno_attachManifestsesameAnno_buildAddressFilesesameAnno_buildManifestGRangessesameAnno_downloadsesameAnno_readManifestTSVsesameQC_calcStatssesameQC_getStatssesameQC_plotBarsesameQC_plotBetaByDesignsesameQC_plotHeatSNPssesameQC_plotIntensVsBetassesameQC_plotRedGrnQQsesameQC_rankStatssesameQCtoDFsetMaskSigDFsignalMUsliceFileSetsummaryExtractTesttotalIntensitiesupdateSigDFvisualizeGenevisualizeProbesvisualizeRegionvisualizeSegments

Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobcachemclicliprcodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArraydplyrExperimentHubfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplyrpngpreprocessCoreprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreadrreshape2rlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfosesameDatasnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwheatmapwithrXVectoryaml

Basic Usage & Preprocessing

Rendered fromsesame.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-01-07
Started: 2018-03-03

Sample Metadata Inference

Rendered frominferences.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-01-07
Started: 2021-06-05

Quality Control

Rendered fromQC.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-01-07
Started: 2019-03-18

Working with Non-human Array

Rendered fromnonhuman.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-01-07
Started: 2021-06-05

Modeling

Rendered frommodeling.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-01-07
Started: 2021-06-05

Readme and manuals

Help Manual

Help pageTopics
Analyze DNA methylation datasesame-package sesame
Add probes to maskaddMask
assemble plotsassemble_plots
Collapse betas by averagng probes with common probe ID prefixbetasCollapseToPfx
Convert beta-value to M-valueBetaValueToMValue
Bin signals from probe signalsbinSignals
Compute internal bisulfite conversion controlbisConversionControl
Compute effect size for different variables from prediction matrixcalcEffectSize
filter data matrix by factor completeness only works for discrete factorscheckLevels
Lookup address in one samplechipAddressToSignal
Perform copy number segmentationcnSegmentation
Compare Strain SNPs with a reference panelcompareMouseStrainReference
Compare array data with references (e.g., tissue, cell types)compareReference
get the controls attributescontrols
Convert Probe IDconvertProbeID
Turn beta values into a UCSC browser trackcreateUCSCtrack
Convert data frame to sesameQC objectdataFrame2sesameQC
De-identify IDATs by removing SNP probesdeIdentify
Detection P-value based on ECDF of negative controldetectionPnegEcdf
Restrict refset to differentially methylated probes use with care, might introduce biasdiffRefSet
List all contrasts of a DMLSummarydmContrasts
Test differential methylation on each locusDML
Predict new data from DMLDMLpredict
Find Differentially Methylated Region (DMR)DMR
Correct dye bias in by linear scaling.dyeBiasCorr
Correct dye bias using most balanced sample as the referencedyeBiasCorrMostBalanced
Correct dye bias in by linear scaling.dyeBiasL
Dye bias correction by matching green and red to mid pointdyeBiasCorrTypeINorm dyeBiasNL
ELiminate BAckground-dominated Reading (ELBAR)ELBAR
Estimate leukocyte fraction using a two-component modelestimateLeukocyte
Convert SNP from Infinium array to VCF fileformatVCF
Get allele frequencygetAFs
Get allele frequency treating type I by summing allelesgetAFTypeIbySumAlleles
Get beta ValuesgetBetas
Get bin coordinatesgetBinCoordinates
get probe masking by mask namesgetMask
Retrieve reference setgetRefSet
Impute of missing data of specific platformimputeBetas
Impute missing data based on genomic neighbors.imputeBetasByGenomicNeighbors
Impute Missing Values with Mean This function replaces missing values (NA) in a matrix, default is row means.imputeBetasMatrixByMean
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.inferInfiniumIChannel
Infer sex.inferSex
Infer SpeciesinferSpecies
Infer strain information for mouse arrayinferStrain
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.inferTissue
initialize a fileSet class by allocating appropriate storageinitFileSet
list existing quality masks for a SigDFlistAvailableMasks
Deposit data of one sample to a fileSet (and hence to file)mapFileSet
Map the SDF (from overlap array platforms) Replicates are merged by picking the best detectionmapToMammal40
normalize Infinium I probe betas to Infinium IImatchDesign
Whole-dataset-wide Mean IntensitymeanIntensity
Whole-dataset-wide Median Total Intensity (M+U)medianTotalIntensity
Lift over beta values or SigDFs to another Infinium platform This function wraps ID conversion and provide optional imputation functionality.mLiftOver
Convert M-value to beta-valueMValueToBetaValue
get negative control signalnegControls
remove masked probes from SigDFnoMasked
Noob background subtractionnoob
get normalization control signalnormControls
The openSesame pipelineopenSesame
openSesame pipeline with file-backed storageopenSesameToFile
Generate some additional color palettespalgen
Convert signal M and U to SigDFparseGEOsignalMU
Detection P-value based on ECDF of out-of-band signalpOOBAH
Predict age using linear modelspredictAge
Mask SigDF by probe ID prefixprefixMask
Mask all but C probes in SigDFprefixMaskButC
Mask all but CG probes in SigDFprefixMaskButCG
Apply a chain of sesame preprocessing functions in an arbitrary orderprepSesame
List supported prepSesame functionsprepSesameList
Print DMLSummary objectprint.DMLSummary
Print a fileSetprint.fileSet
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 illustrationprobeID_designType
Whole-dataset-wide Probe Success RateprobeSuccessRate
Mask beta values by design qualityqualityMask
Read an existing fileSet from storagereadFileSet
Import a pair of IDATs from one samplereadIDATpair
Recommended mask names for each Infinium platformrecommendedMaskNames
Re-identify IDATs by restoring scrambled SNP intensitiesreIdentify
Reset MaskingresetMask
SCRUB background correctionscrub
SCRUB background correctionscrubSoft
read a table file to SigDFsdf_read_table
write SigDF to table filesdf_write_table
collapse to probe prefixSDFcollapseToPfx
Convenience function to output platform attribute of SigDFsdfPlatform
Identify IDATs from a directorysearchIDATprefixes
Segment bins using DNAcopysegmentBins
Check SeSAMe versionssesame_checkVersion
Annotate a data.frame using manifestsesameAnno_attachManifest
Build sesame ordering address file from tsvsesameAnno_buildAddressFile
Build manifest GRanges from tsvsesameAnno_buildManifestGRanges
Download SeSAMe annotation filessesameAnno_download
Read manifest file to a tsv formatsesameAnno_readManifestTSV
Calculate QC statisticssesameQC_calcStats
Get stat numbers from an sesameQC objectsesameQC_getStats
Bar plots for sesameQCsesameQC_plotBar
Plot betas distinguishing different Infinium chemistriessesameQC_plotBetaByDesign
Plot SNP heatmapsesameQC_plotHeatSNPs
Plot Total Signal Intensities vs Beta Values This plot is helpful in revealing the extent of signal background and dye bias.sesameQC_plotIntensVsBetas
Plot red-green QQ-Plot using Infinium-I ProbessesameQC_plotRedGrnQQ
This function compares the input sample with public data. Only overlapping metrics will be compared.sesameQC_rankStats
An S4 class to hold QC statisticssesameQC-class
Convert a list of sesameQC to data framesesameQCtoDF
Set mask to only the probes specifiedsetMask
SigDF validation from a plain data frameSigDF
report M and U for regular probessignalMU
Slice a fileSet with samples and probessliceFileSet
Extract slope information from DMLSummarysummaryExtractTest
M+U Intensities ArraytotalIntensities
Estimate the fraction of the 2nd component in a 2-component mixturetwoCompsEst2
Set color and mask using strain/species-specific manifestupdateSigDF
Visualize GenevisualizeGene
Visualize Region that Contains the Specified ProbesvisualizeProbes
Visualize RegionvisualizeRegion
Visualize segmentsvisualizeSegments