Man pages for zwdzwd/sesame
Tools For Analyzing Illumina Infinium DNA Methylation Arrays

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
ctl-methodsctl getter generic
ctl-replace-methodsctl replacement generic
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
diffRefSetRestrict refset to differentially methylated probes use with...
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
getAFTypeIbySumAllelesGet allele frequency treating type I by summing alleles
getBetasGet beta Values
getBetasTypeIbySumChannelsGet beta values treating type I by summing channels
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
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
IR-methodsIR getter generic
IR-replace-methodsIR replacement generic
makeExampleSeSAMeDataSetMake a simulated SeSAMe data set
makeExampleTinyEPICDataSetMake a tiny toy simulated EPIC data set
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
predictAgeHorvath353Horvath 353 age predictor
predictAgePhenoPhenotypic age predictor
predictAgeSkinBloodHorvath Skin and Blood age predictor
pval-methodspval getter generic
pval-replace-methodsReplace pval slot of SigSet class
readIDATpairImport a pair of IDATs from one sample
reopenSesamere-compute beta value for GenomicRatioSet
searchIDATprefixesIdentify IDATs from a directory
segmentBinsSegment bins using DNAcopy
sesame-packageAnalyze DNA methylation data
sesamize"fix" an RGset (for which IDATs may be unavailable) with...
show-methodsThe display method for SigSet
signalR6toS4sesame R6 to S4
SignalSetSignalSet class
SigSet-classSigSet class
SigSetListconstructor
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'...
SNPcheckCheck sample identity using SNP probes
subsetSignalSelect a subset of probes
totalIntensitiesM+U Intensities for All Probes
totalIntensityZscoreCalculate intensity Z-score
visualizeGeneVisualize Gene
visualizeProbesVisualize Region that Contains the Specified Probes
visualizeRegionVisualize Region
visualizeSegmentsVisualize segments
zwdzwd/sesame documentation built on Sept. 22, 2018, 5:36 p.m.