# SEnsible Step-wise Analysis of DNA MEthylation BeadChips

## Documentation for package ‘sesame’ version 1.8.12

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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

sesame-package | Analyze DNA methylation data

## -- A --

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
detectionMask | Mask Sigset by detection p-value
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
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
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

## -- 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)
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.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
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
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 slope information from DMLSummary
summaryExtractSlope | 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