Tools For Analyzing Illumina Infinium DNA Methylation Arrays


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Documentation for package ‘sesame’ version 1.4.0

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A B C D E G I M N O P R S T V misc

sesame-package Analyze DNA methylation data

-- A --

as.data.frame.sesameQC 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
signalR6toS4 sesame R6 to S4
SignalSet SignalSet class
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

-- V --

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

-- misc --

_PACKAGE Analyze DNA methylation data