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A B C D E F G I M N O P Q R S T V misc
| sesame-package | Analyze DNA methylation data |
| addMask | Add probes to mask |
| as.data.frame.sesameQC | Coerce a sesameQC into a dataframe |
| 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 |
| 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 |
| deIdentify | De-identify IDATs by removing SNP probes |
| 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 |
| 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 |
| dyeBiasNL | Dye bias correction by matching green and red to mid point |
| 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 |
| formatVCF | Convert SNP from Infinium array to VCF file |
| 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 |
| 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 |
| 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) |
| mask | Get current mask of SigSet class |
| meanIntensity | Mean Intensity |
| MValueToBetaValue | Convert M-value to beta-value |
| noob | Noob background correction |
| noobsb | Background subtraction with bleeding-through subtraction |
| 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 |
| 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.DMLSummary | Print DMLSummary object |
| 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 |
| 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 |
| 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) |
| 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 |
| sesamePlotIntensVsBetas | Plot Total Signal Intensities vs Beta Values This plot is helpful in revealing the extent of signal background and dye bias. |
| sesamePlotRedGrnQQ | Plot red-green QQ-Plot using Infinium-I Probes |
| 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 |
| setMask | Set mask to only the probes specified |
| 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 Coefficient Table List from DMLSummary This function returns a list of coefficients for each variable tested. |
| summaryExtractTest | Extract slope information from DMLSummary |
| 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 |
| visualizeGene | Visualize Gene |
| visualizeProbes | Visualize Region that Contains the Specified Probes |
| visualizeRegion | Visualize Region |
| visualizeSegments | Visualize segments |
| _PACKAGE | Analyze DNA methylation data |