Package: sesame 1.25.3

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], Wubin Ding [ctb], David Goldberg [ctb], Ethan Moyer [ctb], Bret Barnes [ctb], Timothy Triche [ctb], Hui Shen [aut]

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# 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-1.25.2(bioc 3.21)sesame-1.24.0(bioc 3.20)

dnamethylation methylationarray preprocessing qualitycontrol bioinformatics dna-methylation microarray

9.16 score 65 stars 1 packages 258 scripts 1.4k downloads 2 mentions 108 exports 103 dependencies

Last updated 14 days agofrom:715da261c4. Checks:2 ERROR, 2 FAILURE, 3 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	FAIL	Jan 05 2025
R-4.5-win	WARNING	Jan 05 2025
R-4.5-linux	ERROR	Jan 05 2025
R-4.4-win	WARNING	Jan 05 2025
R-4.4-mac	WARNING	Jan 05 2025
R-4.3-win	OUTDATED	Dec 01 2024
R-4.3-mac	OUTDATED	Dec 01 2024

Exports:addMask betasCollapseToPfx BetaValueToMValue bisConversionControl calcEffectSize checkLevels cnSegmentation compareMouseStrainReference compareMouseTissueReference compareReference controls createUCSCtrack deIdentify detectionPnegEcdf diffRefSet dmContrasts DML DMLpredict DMR dyeBiasCorr dyeBiasCorrMostBalanced dyeBiasCorrTypeINorm dyeBiasL dyeBiasNL ELBAR estimateLeukocyte formatVCF getAFs getAFTypeIbySumAlleles getBetas getMask getRefSet imputeBetas imputeBetasByGenomicNeighbors imputeBetasMatrixByMean inferEthnicity inferInfiniumIChannel inferSex inferSpecies inferStrain inferTissue initFileSet liftOver listAvailableMasks mapFileSet mapToMammal40 matchDesign meanIntensity medianTotalIntensity mLiftOver MValueToBetaValue noMasked noob openSesame openSesameToFile palgen parseGEOsignalMU pOOBAH predictAge predictAgeHorvath353 predictAgeSkinBlood predictMouseAgeInMonth prefixMask prefixMaskButC prefixMaskButCG prepSesame prepSesameList probeID_designType probeSuccessRate qualityMask readFileSet readIDATpair recommendedMaskNames reIdentify resetMask scrub scrubSoft sdf_read_table sdf_write_table sdfPlatform searchIDATprefixes sesame_checkVersion sesameAnno_attachManifest sesameAnno_buildAddressFile sesameAnno_buildManifestGRanges sesameAnno_download sesameAnno_readManifestTSV sesameQC_calcStats sesameQC_getStats sesameQC_plotBar sesameQC_plotBetaByDesign sesameQC_plotHeatSNPs sesameQC_plotIntensVsBetas sesameQC_plotRedGrnQQ sesameQC_rankStats sesameQCtoDF sesamize setMask SigDF signalMU sliceFileSet summaryExtractTest totalIntensities updateSigDF visualizeGene visualizeProbes visualizeRegion visualizeSegments

Dependencies:abind AnnotationDbi AnnotationHub askpass BH Biobase BiocFileCache BiocGenerics BiocManager BiocParallel BiocVersion Biostrings bit bit64 blob cachem cli clipr codetools colorspace cpp11 crayon curl DBI dbplyr DelayedArray dplyr ExperimentHub fansi farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable hms httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp readr reshape2 rlang RSQLite S4Arrays S4Vectors scales sesameData snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom wheatmap withr XVector yaml

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Help page	Topics
Analyze DNA methylation data	sesame-package sesame
Add probes to mask	addMask
assemble plots	assemble_plots
Collapse betas by averagng probes with common probe ID prefix	betasCollapseToPfx
Convert beta-value to M-value	BetaValueToMValue
Bin signals from probe signals	binSignals
Compute internal bisulfite conversion control	bisConversionControl
Compute effect size for different variables from prediction matrix	calcEffectSize
filter data matrix by factor completeness only works for discrete factors	checkLevels
Lookup address in one sample	chipAddressToSignal
Perform copy number segmentation	cnSegmentation
Compare Strain SNPs with a reference panel	compareMouseStrainReference
Compare mouse array data with mouse tissue references	compareMouseTissueReference
Compare array data with references (e.g., tissue, cell types)	compareReference
get the controls attributes	controls
Convert Probe ID	convertProbeID
Turn beta values into a UCSC browser track	createUCSCtrack
Convert data frame to sesameQC object	dataFrame2sesameQC
De-identify IDATs by removing SNP probes	deIdentify
Detection P-value based on ECDF of negative control	detectionPnegEcdf
Restrict refset to differentially methylated probes use with care, might introduce bias	diffRefSet
List all contrasts of a DMLSummary	dmContrasts
Test differential methylation on each locus	DML
Predict new data from DML	DMLpredict
Find Differentially Methylated Region (DMR)	DMR
Correct dye bias in by linear scaling.	dyeBiasCorr
Correct dye bias using most balanced sample as the reference	dyeBiasCorrMostBalanced
Correct dye bias in by linear scaling.	dyeBiasL
Dye bias correction by matching green and red to mid point	dyeBiasCorrTypeINorm dyeBiasNL
ELiminate BAckground-dominated Reading (ELBAR)	ELBAR
Estimate leukocyte fraction using a two-component model	estimateLeukocyte
Convert SNP from Infinium array to VCF file	formatVCF
Get allele frequency	getAFs
Get allele frequency treating type I by summing alleles	getAFTypeIbySumAlleles
Get beta Values	getBetas
Get bin coordinates	getBinCoordinates
get probe masking by mask names	getMask
Retrieve reference set	getRefSet
Impute of missing data of specific platform	imputeBetas
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 Ethnicity	inferEthnicity
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 Species	inferSpecies
Infer strain information for mouse array	inferStrain
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 storage	initFileSet
liftOver, see mLiftOver (renamed)	liftOver
list existing quality masks for a SigDF	listAvailableMasks
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 detection	mapToMammal40
normalize Infinium I probe betas to Infinium II	matchDesign
Whole-dataset-wide Mean Intensity	meanIntensity
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-value	MValueToBetaValue
get negative control signal	negControls
remove masked probes from SigDF	noMasked
Noob background subtraction	noob
get normalization control signal	normControls
The openSesame pipeline	openSesame
openSesame pipeline with file-backed storage	openSesameToFile
Generate some additional color palettes	palgen
Convert signal M and U to SigDF	parseGEOsignalMU
Detection P-value based on ECDF of out-of-band signal	pOOBAH
Predict age using linear models	predictAge
Horvath 353 age predictor	predictAgeHorvath353
Horvath Skin and Blood age predictor	predictAgeSkinBlood
Mouse age predictor	predictMouseAgeInMonth
Mask SigDF by probe ID prefix	prefixMask
Mask all but C probes in SigDF	prefixMaskButC
Mask all but CG probes in SigDF	prefixMaskButCG
Apply a chain of sesame preprocessing functions in an arbitrary order	prepSesame
List supported prepSesame functions	prepSesameList
Print DMLSummary object	print.DMLSummary
Print a fileSet	print.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 illustration	probeID_designType
Whole-dataset-wide Probe Success Rate	probeSuccessRate
Mask beta values by design quality	qualityMask
Read an existing fileSet from storage	readFileSet
Import a pair of IDATs from one sample	readIDATpair
Recommended mask names for each Infinium platform	recommendedMaskNames
Re-identify IDATs by restoring scrambled SNP intensities	reIdentify
Reset Masking	resetMask
SCRUB background correction	scrub
SCRUB background correction	scrubSoft
read a table file to SigDF	sdf_read_table
write SigDF to table file	sdf_write_table
collapse to probe prefix	SDFcollapseToPfx
Convenience function to output platform attribute of SigDF	sdfPlatform
Identify IDATs from a directory	searchIDATprefixes
Segment bins using DNAcopy	segmentBins
Check SeSAMe versions	sesame_checkVersion
Annotate a data.frame using manifest	sesameAnno_attachManifest
Build sesame ordering address file from tsv	sesameAnno_buildAddressFile
Build manifest GRanges from tsv	sesameAnno_buildManifestGRanges
Download SeSAMe annotation files	sesameAnno_download
Read manifest file to a tsv format	sesameAnno_readManifestTSV
Calculate QC statistics	sesameQC_calcStats
Get stat numbers from an sesameQC object	sesameQC_getStats
Bar plots for sesameQC	sesameQC_plotBar
Plot betas distinguishing different Infinium chemistries	sesameQC_plotBetaByDesign
Plot SNP heatmap	sesameQC_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 Probes	sesameQC_plotRedGrnQQ
This function compares the input sample with public data. Only overlapping metrics will be compared.	sesameQC_rankStats
An S4 class to hold QC statistics	sesameQC-class
Convert a list of sesameQC to data frame	sesameQCtoDF
sesamize function is deprecated. Please check https://github.com/zwdzwd/sesamize for previous scripts	sesamize
Set mask to only the probes specified	setMask
SigDF validation from a plain data frame	SigDF
report M and U for regular probes	signalMU
Slice a fileSet with samples and probes	sliceFileSet
Extract slope information from DMLSummary	summaryExtractTest
M+U Intensities Array	totalIntensities
Estimate the fraction of the 2nd component in a 2-component mixture	twoCompsEst2
Set color and mask using strain/species-specific manifest	updateSigDF
Visualize Gene	visualizeGene
Visualize Region that Contains the Specified Probes	visualizeProbes
Visualize Region	visualizeRegion
Visualize segments	visualizeSegments

Package: sesame 1.25.3

sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

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