A B C D E G I M N O P R S T V misc
sesame-package | Analyze DNA methylation data |
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 |
ctl | ctl getter generic |
ctl-method | ctl getter generic |
ctl<- | ctl replacement generic |
ctl<--method | ctl replacement generic |
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 |
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 |
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 |
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 | IG getter generic |
IG-method | IG getter generic |
IG<- | IG replacement generic |
IG<--method | IG replacement generic |
II | II getter generic |
II-method | II getter generic |
II<- | II replacement generic |
II<--method | 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 using what is specified in manifest |
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 |
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 | oobG getter generic |
oobG-method | oobG getter generic |
oobG<- | oobG replacement generic |
oobG<--method | oobG replacement generic |
oobR | oobR getter generic |
oobR-method | oobR getter generic |
oobR<- | oobR replacement generic |
oobR<--method | 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 |
pOOBAH | 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 |
print.fileSet | Print a fileSet |
print.sesameQC | Print sesameQC object |
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 |
readFileSet | Read an existing fileSet from storage |
readIDATpair | Import a pair of IDATs from one sample |
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 | Analyze DNA methylation data |
sesameQC | Generate summary numbers that indicative of experiment quality |
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 |
signalR6toS4 | sesame R6 to S4 |
SignalSet | SignalSet class |
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 |
topLoci | Top loci in differential methylation |
topSegments | Top segments in differential methylation |
totalIntensities | M+U Intensities for All Probes |
totalIntensityZscore | Calculate intensity Z-score |
visualizeGene | Visualize Gene |
visualizeProbes | Visualize Region that Contains the Specified Probes |
visualizeRegion | Visualize Region |
visualizeSegments | Visualize segments |
_PACKAGE | Analyze DNA methylation data |