SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Documentation for package ‘sesame’ version 1.20.0

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A B C D E F G I K L M N O P Q R S T U V misc

Analyze DNA methylation data

-- A --

addMask	Add probes to mask
aggregateTestEnrichments	Aggregate test enrichment results
assemble_plots	assemble plots

-- B --

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

-- C --

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
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
compareReference	Compare array data with references (e.g., tissue, cell types)
controls	get the controls attributes
convertTo	Convert human arrays to previous platforms Missing probes are replaced using NAs.
createDBNetwork	createGeneNetwork creates database network using the Jaccard index.
createUCSCtrack	Turn beta values into a UCSC browser track

-- D --

dataFrame2sesameQC	Convert data frame to sesameQC object
dbStats	dbStats builds dataset for a given betas matrix composed of engineered features from the given database sets
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
dyeBiasCorrTypeINorm	Dye bias correction by matching green and red to mid point
dyeBiasL	Correct dye bias in by linear scaling.
dyeBiasNL	Dye bias correction by matching green and red to mid point

-- E --

ELBAR	ELiminate BAckground-dominated Reading (ELBAR)
estimateCellComposition	Estimate cell composition using reference
estimateLeukocyte	Estimate leukocyte fraction using a two-component model

-- F --

formatVCF

Convert SNP from Infinium array to VCF file

-- G --

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
getSexInfo	Get sex-related information

-- I --

imputeTo	Impute to platform
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	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

-- K --

KYCG_annoProbes	Annotate Probe IDs using KYCG databases
KYCG_buildGeneDBs	build gene-probe association database
KYCG_getDBs	Get databases by full or partial names of the database group(s)
KYCG_listDBGroups	List database group names
KYCG_loadDBs	Load database groups
KYCG_plotBar	Bar plot to show most enriched CG groups from testEnrichment
KYCG_plotDot	Dot plot to show most enriched CG groups from testEnrichment
KYCG_plotEnrichAll	plot enrichment test result
KYCG_plotLollipop	creates a lollipop plot of log(estimate) given data with fields estimate.
KYCG_plotManhattan	KYCG_plotManhattan makes a manhattan plot to summarize EWAS results
KYCG_plotMeta	Plot meta gene or other meta genomic features
KYCG_plotMetaEnrichment	Plot meta gene or other meta genomic features
KYCG_plotPointRange	Plot point range for a list of enrichment testing results against the same set of databases
KYCG_plotSetEnrichment	Plot Set Enrichment
KYCG_plotVolcano	creates a volcano plot of -log2(p.value) and log(estimate) given data with fields estimate and p.value.
KYCG_plotWaterfall	create a waterfall plot of log(estimate) given test enrichment

-- L --

listAvailableMasks

list existing quality masks for a SigDF

-- M --

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)
MValueToBetaValue	Convert M-value to beta-value

-- N --

negControls	get negative control signal
noMasked	remove masked probes from SigDF
noob	Noob background subtraction
normControls	get normalization control signal

-- O --

openSesame	The openSesame pipeline
openSesameToFile	openSesame pipeline with file-backed storage

-- P --

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
predictAgeHorvath353	Horvath 353 age predictor
predictAgeSkinBlood	Horvath Skin and Blood age predictor
predictMouseAgeInMonth	Mouse age predictor
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

-- Q --

qualityMask

Mask beta values by design quality

-- R --

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

-- S --

scrub	SCRUB background correction
scrubSoft	SCRUB background correction
SDFcollapseToPfx	collapse to probe prefix
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	Analyze DNA methylation data
sesameAnno_buildAddressFile	Build sesame ordering address file from tsv
sesameAnno_buildManifestGRanges	Build manifest GRanges from tsv
sesameAnno_download	Download SeSAMe annotation files
sesameAnno_get	download Infinium manifest from the associated Github repository
sesameAnno_readManifestTSV	Read manifest file to a tsv format
sesameData_getAnno	retrieve additional annotation files
sesameQC-class	An S4 class to hold QC statistics
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.
sesame_checkVersion	Check SeSAMe versions
sesamize	sesamize function is deprecated. Please check https://github.com/zwdzwd/sesamize for previous scripts
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

-- T --

testEnrichment	testEnrichment tests for the enrichment of set of probes (query set) in a number of features (database sets).
testEnrichmentFisher	testEnrichmentFisher uses Fisher's exact test to estimate the association between two categorical variables.
testEnrichmentGene	Convenient function for testing enrichment of gene linkage
testEnrichmentSEA	uses the GSEA-like test to estimate the association of a categorical variable against a continuous variable.
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

-- U --

updateSigDF

Set color and mask using strain/species-specific manifest

-- V --

visualizeGene	Visualize Gene
visualizeProbes	Visualize Region that Contains the Specified Probes
visualizeRegion	Visualize Region
visualizeSegments	Visualize segments

-- misc --

_PACKAGE

Analyze DNA methylation data