SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Documentation for package ‘sesame’ version 1.12.1

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Analyze DNA methylation data

-- A --

addMask	Add probes to mask
as.data.frame.sesameQC	Coerce a sesameQC into a dataframe
attachManifest	Annotate a data.frame using manifest

-- B --

BetaValueToMValue	Convert beta-value to M-value
binSignals	Bin signals from probe signals
bisConversionControl	Compute internal bisulfite conversion control
bSubComplete	subset beta value matrix by complete probes
bSubMostVariable	Get most variable probes
bSubProbes	subset beta value matrix by probes

-- C --

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

-- D --

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
DML	Test differential methylation on each locus
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
dyeBiasDistortion	Quantify how much dye bias in high signal range deviates from the global median
dyeBiasNL	Dye bias correction by matching green and red to mid point

-- E --

estimateCellComposition	Estimate cell composition using reference
estimateLeukocyte	Estimate leukocyte fraction using a two-component model
extractDesign	Extract the first design category

-- F --

formatVCF

Convert SNP from Infinium array to VCF file

-- G --

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

-- I --

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

-- M --

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)
MValueToBetaValue	Convert M-value to beta-value

-- N --

neob	Negative control plus out-of-band background correction
noMasked	remove masked probes from SigDF
noob	Noob background correction

-- O --

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

-- P --

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.
pOOBAH	Detection P-value based on ECDF of out-of-band signal
pOOBAH2	Detection P-value based on ECDF of out-of-band signal
predictAgeHorvath353	Horvath 353 age predictor
predictAgeSkinBlood	Horvath Skin and Blood age predictor
predictMouseAgeInMonth	Mouse age predictor
print.DMLSummary	Print DMLSummary object
print.fileSet	Print a fileSet
print.sesameQC	Print sesameQC object
print.SigDF	Print SigDF 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

-- Q --

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

-- R --

readFileSet	Read an existing fileSet from storage
readIDATpair	Import a pair of IDATs from one sample
reIdentify	Re-identify IDATs by restoring scrambled SNP intensities
reopenSesame	re-compute beta value for GenomicRatioSet
resetMask	Reset Masking
RGChannelSetToSigDFs	Convert RGChannelSet (minfi) to a list of SigDF (SeSAMe)

-- S --

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	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
SigDF	SigDF constructor from a plain data frame
SigDFsToRGChannelSet	Convert sesame::SigDF to minfi::RGChannelSet
SigDFToRatioSet	Convert one sesame::SigDF to minfi::RatioSet
signalMU	report M and U for regular probes
sliceFileSet	Slice a fileSet with samples and probes
SNPcheck	Check sample identity using SNP 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).
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

-- V --

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

-- misc --

_PACKAGE

Analyze DNA methylation data