SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Documentation for package ‘sesame’ version 1.10.5

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Analyze DNA methylation data

-- A --

addMask	Add probes to mask
as.data.frame.sesameQC	Coerce a sesameQC into a dataframe

-- B --

betaToAF	convert betas to variant allele frequency
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
buildControlMatrix450k	Build control summary matrix

-- C --

checkLevels	filter data matrix by factor completeness
chipAddressToSignal	Lookup address in one sample
cnSegmentation	Perform copy number segmentation
compareMouseBloodReference	Compare beta value against mouse blood reference
compareMouseTissueReference	Compare mouse array data with mouse tissue references
createUCSCtrack	Turn beta values into a UCSC browser track
ctl	ctl getter generic
ctl-method	ctl getter generic
ctl<-	ctl replacement generic
ctl<--method	ctl replacement generic

-- D --

deIdentify	De-identify IDATs by removing SNP probes
detectionPfixedNorm	Detection P-value based on normal fitting with gived parameters
detectionPnegEcdf	Detection P-value based on ECDF of negative control
detectionPnegNorm	Detection P-value based on normal fitting the negative controls
detectionPnegNormGS	Detection P-value emulating Genome Studio
detectionPnegNormTotal	Detection P-value based on normal fitting the negative controls, channels are first summed
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
DML	Test differential methylation on each locus
DMLShrinkage	Test differential methylation on each locus Using Shrinkage Estimator
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
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
extra	extra getter generic
extra-method	extra getter generic
extra<-	extra replacement generic
extra<--method	extra replacement generic
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
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 --

IG	IG getter generic
IG-method	IG getter generic
IG<-	IG replacement generic
IG<--method	IG replacement generic
IGpass	Get IG slot of SigSet class that passes mask This is the same as IG() if there is no mask set
II	II getter generic
II-method	II getter generic
II<-	II replacement generic
II<--method	II replacement generic
IIpass	Get II slot of SigSet class that passes mask This is the same as II() if there is no mask set
inferEthnicity	Infer Ethnicity
inferSex	Infer Sex
inferSexKaryotypes	Infer Sex Karyotype
inferStrain	Infer strain information for mouse array
inferTypeIChannel	Infer and reset color channel for Type-I probes instead of using what is specified in manifest. The results are stored to sset@extra$IGG and sset@extra$IRR slot.
initFileSet	initialize a fileSet class by allocating appropriate storage
initialize-method	SigSet class
IR	IR getter generic
IR-method	IR getter generic
IR<-	IR replacement generic
IR<--method	IR replacement generic
IRpass	Get IR slot of SigSet class that passes mask This is the same as IR() if there is no mask set
isUniqProbeID	Whether the probe ID is the uniq probe ID like in the mouse array, e.g., cg36609548

-- M --

makeExampleSeSAMeDataSet	Make a simulated SeSAMe data set
makeExampleTinyEPICDataSet	Make a tiny toy simulated EPIC data set
mapFileSet	Deposit data of one sample to a fileSet (and hence to file)
mask	Get current mask of SigSet class
meanIntensity	Mean Intensity
MValueToBetaValue	Convert M-value to beta-value

-- N --

noob	Noob background correction
noobsb	Background subtraction with bleeding-through subtraction

-- O --

oobG	oobG getter generic
oobG-method	oobG getter generic
oobG<-	oobG replacement generic
oobG<--method	oobG replacement generic
oobGpass	Get oobG slot of SigSet class that passes mask This is the same as oobG() if there is no mask set
oobR	oobR getter generic
oobR-method	oobR getter generic
oobR<-	oobR replacement generic
oobR<--method	oobR replacement generic
oobRpass	Get oobR slot of SigSet class that passes mask This is the same as oobR() if there is no mask set
openSesame	The openSesame pipeline
openSesameToFile	openSesame pipeline with file-backed storage

-- P --

parseGEOSignalABFile	Parse GEO signal-A/B File into a SigSet List
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
predictAgePheno	Phenotypic 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
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
probeNames	Get Probe Names of SigSet class
probeNames-method	Get Probe Names of SigSet class
pval	pval getter generic
pval-method	pval getter generic
pval<-	pval replacement generic
pval<--method	pval replacement generic

-- 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
restoreMask	Save current mask
RGChannelSetToSigSets	Convert RGChannelSet (minfi) to a list of SigSet (SeSAMe)

-- S --

saveMask	Save current mask
scrub	SCRUB background correction
scrubSoft	SCRUB background correction
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 sigset (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
show-method	SigSetList methods (centralized). Currently scarce... 'show' print a summary of the SigSetList.
show-method	The display method for SigSet
signalMU	report M and U for regular probes
SigSet	SigSet class
SigSet-class	SigSet class
SigSetList	constructor
SigSetList-class	a List of SigSets with some methods of its own
SigSetList-methods	SigSetList methods (centralized). Currently scarce... 'show' print a summary of the SigSetList.
SigSetListFromIDATs	read IDATs into a SigSetList
SigSetListFromPath	read an entire directory's worth of IDATs into a SigSetList
SigSetsToRGChannelSet	Convert sesame::SigSet to minfi::RGChannelSet
SigSetToRatioSet	Convert one sesame::SigSet to minfi::RatioSet
sliceFileSet	Slice a fileSet with samples and probes
SNPcheck	Check sample identity using SNP probes
subsetSignal	Select a subset of probes
summaryExtractCfList	Extract Coefficient Table List from DMLSummary This function returns a list of coefficients for each variable tested.
summaryExtractTest	Extract slope information from DMLSummary

-- T --

topSegments	Top segments in differential methylation
totalIntensities	M+U Intensities for All Probes
totalIntensityZscore	Calculate intensity Z-score
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