API for haowulab/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
dbb 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
rnegbinom Source code
rowVars Source code Source code
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
haowulab/DSS documentation built on Nov. 8, 2017, 11:53 a.m.