Man pages for sesame
Tools For Analyzing Illumina Infinium DNA Methylation Arrays a sesameQC into a dataframe
BetaValueToMValueConvert beta-value to M-value
binSignalsBin signals from probe signals
bisConversionControlCompute internal bisulfite conversion control
buildControlMatrix450kBuild control summary matrix
chipAddressToSignalLookup address in one sample
cnSegmentationPerform copy number segmentation
createUCSCtrackTurn beta values into a UCSC browser track
ctl-methodsctl getter generic
ctl-replace-methodsctl replacement generic
deidentifyDe-identify IDATs by removing SNP probes
detectionMaskMask Sigset by detection p-value
detectionPfixedNormDetection P-value based on normal fitting with gived...
detectionPnegEcdfDetection P-value based on ECDF of negative control
detectionPnegNormDetection P-value based on normal fitting the negative...
detectionPnegNormGSDetection P-value emulating Genome Studio
detectionPnegNormTotalDetection P-value based on normal fitting the negative...
detectionPoobEcdfDetection P-value based on ECDF of out-of-band signal
detectionZeroDetection P-value set to all zero
diffRefSetRestrict refset to differentially methylated probes use with...
DMLTest differential methylation on each locus
DMRFind Differentially Methylated Region (DMR)
dyeBiasCorrCorrect dye bias in by linear scaling.
dyeBiasCorrMostBalancedCorrect dye bias using most balanced sample as the reference
dyeBiasCorrTypeINormDye bias correction by matching green and red to mid point
estimateCellCompositionEstimate cell composition using reference
estimateLeukocyteEstimate leukocyte fraction using a two-component model
extra-methodsextra getter generic
extra-replace-methodsextra replacement generic
formatVCFConvert SNP from Infinium array to VCF file
getAFTypeIbySumAllelesGet allele frequency treating type I by summing alleles
getBetasGet beta Values
getBinCoordinatesGet bin coordinates
getNormCtlsget normalization control signal
getProbesByGeneGet Probes by Gene
getProbesByRegionGet probes by genomic region
getProbesByTSSGet Probes by Gene Transcription Start Site (TSS)
getRefSetRetrieve reference set
getSegmentSelect segment from coefficient table
getSexInfoGet sex-related information
IG-methodsIG getter generic
IG-replace-methodsIG replacement generic
II-methodsII getter generic
II-replace-methodsII replacement generic
inferEthnicityInfer Ethnicity
inferSexInfer Sex
inferSexKaryotypesInfer Sex Karyotype
inferTypeIChannelInfer and reset color channel for Type-I probes instead of...
initFileSetinitialize a fileSet class by allocating appropriate storage
IR-methodsIR getter generic
IR-replace-methodsIR replacement generic
makeExampleSeSAMeDataSetMake a simulated SeSAMe data set
makeExampleTinyEPICDataSetMake a tiny toy simulated EPIC data set
mapFileSetDeposit data of one sample to a fileSet (and hence to file)
meanIntensityMean Intensity
MValueToBetaValueConvert M-value to beta-value
noobNoob background correction
noobsbBackground subtraction with bleeding-through subtraction
oobG-methodsoobG getter generic
oobG-replace-methodsoobG replacement generic
oobR-methodsoobR getter generic
oobR-replace-methodsoobR replacement generic
openSesameThe openSesame pipeline
openSesameToFileopenSesame pipeline with file-backed storage
parseGEOSignalABFileParse GEO signal-A/B File into a SigSet List
predictAgeHorvath353Horvath 353 age predictor
predictAgePhenoPhenotypic age predictor
predictAgeSkinBloodHorvath Skin and Blood age predictor
print.fileSetPrint a fileSet
print.sesameQCPrint sesameQC object
probeNames-methodsGet Probe Names of SigSet class
pval-methodspval getter generic
pval-replace-methodspval replacement generic
qualityMaskMask beta values by design quality
qualityRankThis function looks at public data of similar nature e.g.,...
readFileSetRead an existing fileSet from storage
readIDATpairImport a pair of IDATs from one sample
reIdentifyRe-identify IDATs by restoring scrambled SNP intensities
reopenSesamere-compute beta value for GenomicRatioSet
RGChannelSetToSigSetsConvert RGChannelSet (minfi) to a list of SigSet (SeSAMe)
searchIDATprefixesIdentify IDATs from a directory
segmentBinsSegment bins using DNAcopy
sesame-packageAnalyze DNA methylation data
sesameQCGenerate summary numbers that indicative of experiment...
sesamize"fix" an RGChannelSet (for which IDATs may be unavailable)...
show-methodsThe display method for SigSet
signalMUreport M and U for regular probes
SigSet-classSigSet class
SigSetList-classa List of SigSets with some methods of its own
SigSetListFromIDATsread IDATs into a SigSetList
SigSetListFromPathread an entire directory's worth of IDATs into a SigSetList
SigSetList-methodsSigSetList methods (centralized). Currently scarce... 'show'...
SigSetsToRGChannelSetConvert sesame::SigSet to minfi::RGChannelSet
SigSetToRatioSetConvert one sesame::SigSet to minfi::RatioSet
sliceFileSetSlice a fileSet with samples and probes
SNPcheckCheck sample identity using SNP probes
subsetSignalSelect a subset of probes
topLociTop loci in differential methylation
topSegmentsTop segments in differential methylation
totalIntensitiesM+U Intensities for All Probes
totalIntensityZscoreCalculate intensity Z-score
twoCompsEst2Estimate the fraction of the 2nd component in a 2-component...
visualizeGeneVisualize Gene
visualizeProbesVisualize Region that Contains the Specified Probes
visualizeRegionVisualize Region
visualizeSegmentsVisualize segments
sesame documentation built on Nov. 15, 2020, 2:08 a.m.