Tools For Analyzing Illumina Infinium DNA Methylation Arrays

Documentation for package ‘sesame’ version 1.5.3

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Analyze DNA methylation data

-- A --

Coerce a sesameQC into a dataframe

-- B --

BetaValueToMValue	Convert beta-value to M-value
binSignals	Bin signals from probe signals
bisConversionControl	Compute internal bisulfite conversion control
buildControlMatrix450k	Build control summary matrix

-- C --

chipAddressToSignal	Lookup address in one sample
cnSegmentation	Perform copy number segmentation
ctl	ctl getter generic
ctl-method	ctl getter generic
ctl<-	ctl replacement generic
ctl<--method	ctl replacement generic

-- D --

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
detectionZero	Detection P-value set to all zero
diffRefSet	Restrict refset to differentially methylated probes use with care, might introduce bias
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

-- E --

estimateCellComposition	Estimate cell composition using reference
estimateLeukocyte	Estimate leukocyte fraction using a two-component model

-- G --

getAFTypeIbySumAlleles	Get allele frequency treating type I by summing alleles
getBetas	Get beta Values
getBinCoordinates	Get bin coordinates
getNormCtls	get normalization control signal
getProbesByGene	Get Probes by Gene
getProbesByRegion	Get probes by genomic region
getProbesByTSS	Get Probes by Gene Transcription Start Site (TSS)
getRefSet	Retrieve reference set
getSegment	Select segment from coefficient table
getSexInfo	Get sex-related information

-- I --

IG	IG getter generic
IG-method	IG getter generic
IG<-	IG replacement generic
IG<--method	IG replacement generic
II	II getter generic
II-method	II getter generic
II<-	II replacement generic
II<--method	II replacement generic
inferEthnicity	Infer Ethnicity
inferSex	Infer Sex
inferSexKaryotypes	Infer Sex Karyotype
inferTypeIChannel	Infer and reset color channel for Type-I probes instead of using what is specified in manifest
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

-- 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)
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
oobR	oobR getter generic
oobR-method	oobR getter generic
oobR<-	oobR replacement generic
oobR<--method	oobR replacement generic
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
predictAgeHorvath353	Horvath 353 age predictor
predictAgePheno	Phenotypic age predictor
predictAgeSkinBlood	Horvath Skin and Blood age predictor
print.fileSet	Print a fileSet
print.sesameQC	Print sesameQC object
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

-- R --

readFileSet	Read an existing fileSet from storage
readIDATpair	Import a pair of IDATs from one sample
reopenSesame	re-compute beta value for GenomicRatioSet
RGChannelSetToSigSets	Convert RGChannelSet (minfi) to a list of SigSet (SeSAMe)

-- S --

searchIDATprefixes	Identify IDATs from a directory
segmentBins	Segment bins using DNAcopy
sesame	Analyze DNA methylation data
sesameQC	Generate summary numbers that indicative of experiment quality
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
show-method	SigSetList methods (centralized). Currently scarce... 'show' print a summary of the SigSetList.
show-method	The display method for SigSet
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

-- T --

topLoci	Top loci in differential methylation
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 --

Analyze DNA methylation data