Man pages for sesame
Tools For Analyzing Illumina Infinium DNA Methylation Arrays
| as.data.frame.sesameQC | Coerce a sesameQC into a dataframe |
| BetaValueToMValue | Convert beta-value to M-value |
| binSignals | Bin signals from probe signals |
| bisConversionControl | Compute internal bisulfite conversion control |
| buildControlMatrix450k | Build control summary matrix |
| chipAddressToSignal | Lookup address in one sample |
| cnSegmentation | Perform copy number segmentation |
| createUCSCtrack | Turn beta values into a UCSC browser track |
| ctl-methods | ctl getter generic |
| ctl-replace-methods | ctl replacement generic |
| 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... |
| detectionPnegEcdf | Detection P-value based on ECDF of negative control |
| detectionPnegNorm | Detection P-value based on normal fitting the negative... |
| detectionPnegNormGS | Detection P-value emulating Genome Studio |
| detectionPnegNormTotal | Detection P-value based on normal fitting the negative... |
| 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... |
| 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 |
| estimateCellComposition | Estimate cell composition using reference |
| estimateLeukocyte | Estimate leukocyte fraction using a two-component model |
| extra-methods | extra getter generic |
| extra-replace-methods | extra replacement generic |
| formatVCF | Convert SNP from Infinium array to VCF file |
| 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 |
| IG-methods | IG getter generic |
| IG-replace-methods | IG replacement generic |
| II-methods | II getter generic |
| II-replace-methods | 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... |
| initFileSet | initialize a fileSet class by allocating appropriate storage |
| IR-methods | IR getter generic |
| IR-replace-methods | IR replacement generic |
| 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 |
| noob | Noob background correction |
| noobsb | Background subtraction with bleeding-through subtraction |
| oobG-methods | oobG getter generic |
| oobG-replace-methods | oobG replacement generic |
| oobR-methods | oobR getter generic |
| oobR-replace-methods | oobR replacement generic |
| openSesame | The openSesame pipeline |
| openSesameToFile | openSesame pipeline with file-backed storage |
| parseGEOSignalABFile | Parse GEO signal-A/B File into a SigSet List |
| 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-methods | Get Probe Names of SigSet class |
| pval-methods | pval getter generic |
| pval-replace-methods | pval replacement generic |
| qualityMask | Mask beta values by design quality |
| qualityRank | This function looks at public data of similar nature e.g.,... |
| 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 |
| RGChannelSetToSigSets | Convert RGChannelSet (minfi) to a list of SigSet (SeSAMe) |
| searchIDATprefixes | Identify IDATs from a directory |
| segmentBins | Segment bins using DNAcopy |
| sesame-package | Analyze DNA methylation data |
| sesameQC | Generate summary numbers that indicative of experiment... |
| sesamize | "fix" an RGChannelSet (for which IDATs may be unavailable)... |
| show-methods | The display method for SigSet |
| signalMU | report M and U for regular probes |
| SigSet-class | SigSet class |
| SigSetList | constructor |
| SigSetList-class | a List of SigSets with some methods of its own |
| SigSetListFromIDATs | read IDATs into a SigSetList |
| SigSetListFromPath | read an entire directory's worth of IDATs into a SigSetList |
| SigSetList-methods | SigSetList methods (centralized). Currently scarce... 'show'... |
| 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 |
| topLoci | Top loci in differential methylation |
| 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... |
| visualizeGene | Visualize Gene |
| visualizeProbes | Visualize Region that Contains the Specified Probes |
| visualizeRegion | Visualize Region |
| visualizeSegments | Visualize segments |
