API for DSS
Dispersion shrinkage for sequencing data
| Global functions | |
|---|---|
| DMLfit.multiFactor | Man page Source code |
| DMLfit.multiFactor.engine | Source code |
| DMLfit.oneCG | Source code |
| DMLtest | Man page Source code |
| DMLtest.Smooth | Source code |
| DMLtest.multiFactor | Man page Source code |
| DMLtest.multiFactor.Contrast | Source code |
| DMLtest.multiFactor.coef | Source code |
| DMLtest.noSmooth | Source code |
| DSS | Man page |
| DSS-package | Man page |
| DSS.DE | Man page Source code |
| RRBS | Man page |
| SeqCountSet | Man page |
| SeqCountSet-class | Man page |
| calc.expY | Source code |
| callDML | Man page Source code |
| callDMR | Man page Source code |
| compute.baseSigma.notrend | Source code |
| compute.baseSigma.trend | Source code |
| compute.mean.Smooth | Source code |
| compute.mean.noSmooth | Source code |
| compute.var.Smooth | Source code |
| compute.var.Smooth.old | Source code |
| compute.waldStat.Smooth | Source code |
| compute.waldStat.noSmooth | Source code |
| design | Man page |
| dispersion | Man page |
| dispersion,SeqCountSet-method | Man page |
| dispersion.shrinkage.BSseq | Source code |
| dispersion<- | Man page |
| dispersion<-,SeqCountSet,numeric-method | Man page |
| est.dispersion | Source code |
| est.dispersion.BSseq | Source code |
| est.phi.naive | Source code |
| est.phi0 | Source code |
| est.prior.BSseq.logN | Source code |
| est.trend | Source code |
| estDispersion | Man page Source code |
| estDispersion,SeqCountSet-method | Man page |
| estDispersion.multiFactor | Source code |
| estDispersion.notrend | Source code |
| estDispersion.trend | Source code |
| estNormFactors | Man page Source code |
| estNormFactors,SeqCountSet-method | Man page |
| estNormFactors.lr | Source code |
| estNormFactors.median | Source code |
| estNormFactors.quantile | Source code |
| estNormFactors.total | Source code |
| findBumps | Source code |
| findRegion | Source code |
| getBSseqIndex | Source code |
| hasCoverage | Source code |
| loccov | Source code |
| loccov2 | Source code |
| locfdr | Source code |
| locmle | Source code |
| lrTest | Source code |
| makeBSseqData | Man page Source code |
| makeContrast | Source code |
| makeDesign | Source code |
| mergeData.counts | Source code |
| mergeData.counts.smooth | Source code |
| newSeqCountSet | Man page Source code |
| normalizationFactor | Man page |
| normalizationFactor,SeqCountSet-method | Man page |
| normalizationFactor<- | Man page |
| normalizationFactor<-,SeqCountSet,matrix-method | Man page |
| normalizationFactor<-,SeqCountSet,numeric-method | Man page |
| scv | Source code |
| seqData | Man page |
| showOneDMR | Man page Source code |
| shrink.dispersion.notrend | Source code |
| shrink.dispersion.trend | Source code |
| smooth.chr | Source code |
| smooth.collapse | Source code |
| sortPos | Source code |
| waldTest | Man page Source code |
| waldTest,SeqCountSet-method | Man page |
| waldTest.DML | Source code |
