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 |