Man pages for JohnReid/DeLorean
Estimates Pseudotimes for Single Cell Expression Data

adjust.by.cell.sizesAdjust the expression by the estimated cell sizes.
alpha.for.rugCalculate a suitable value for a rug plot given the number of...
analyse.noise.levelsAnalyse noise levels and assess which genes have the greatest...
analyse.varianceAnalyse variance of expression between and within capture...
anders.huber.cell.sizesEstimate the cell sizes according to Anders & Huber...
aov.dlPerform an analysis of variance to select genes for the...
avg.par.samplesAverage across a parameters samples.
calc.inducing.pseudotimesCalculate inducing pseudotimes for sparse approximation
calc.roughnessCalculate the roughness of the vector. The roughness is the...
centraliseCentralises a periodic position into [period/2, period) by...
cmp.profiles.plotPlot a comparison of the profiles from several de.lorean...
compile.modelCompile the model and cache the DSO to avoid unnecessary...
cov.all.genes.conditionedCalculate covariances for all genes when conditioned on data...
cov.calc.distsCalculate distances between vectors of time points
cov.calc.dl.distsCalculate distances over estimated pseudotimes and test...
cov.calc.geneCalculate covariance structure for gene over pseudotimes and...
cov.calc.gene.conditionedCalculate covariance for gene over test inputs when...
cov.matern.32Matern 3/2 covariance function
cov.periodiseMakes a distance periodic
create.ordering.ll.fnCalculate the covariance structure of evenly spread tau and...
default.num.coresDefault number of cores to use.
de.loreanInitialise DeLorean object
DeLoreanDeLorean.
de.lorean.stylesheetThe filename of the R markdown stylesheet
dim.de.loreanDimensions of DeLorean object
estimate.cell.sizesEstimate the cell sizes. We only consider genes that are...
estimate.hyperEstimate hyperparameters for model using empirical Bayes.
examine.convergenceAnalyse the samples and gather the convergence statistics....
expected.sample.varThe expected within sample variance of a Gaussian with the...
expr.data.plotPlot the expression data by the capture points
filter_cellsFilter cells
filter.cellsFilter cells
filter_genesFilter genes
filter.genesFilter genes
find.best.tauFind best tau to initialise chains with by sampling tau from...
find.good.orderingRun a find good ordering method and append results to...
find.smooth.tauFind best order of the samples assuming some smooth GP prior...
fit.dlPerform all the steps necessary to fit the model. - prepare...
fit.held.outFit held out genes
fit.modelFit the model using specified method (sampling or variational...
fit.model.sampleFit the model using Stan sampler
fit.model.vbFit the model using Stan variational Bayes
gaussian.conditionCondition a Guassian on another. See Eqn. A.6 on page 200 of...
gene.covariancesCalculate the covariance structure of the tau
get.posterior.meanGet posterior mean of samples
gp.log.marg.likeThe log marginal likelihood. See "2.3 Varying the...
gp.predictPredictive mean, variance and log marginal likelihood of a...
gp.predictions.dfConvert the output of gp.predict() into a data.frame.
guo.exprSingle cell expression data and meta data from Guo et al....
held.out.meltMelt held out genes
held.out.posteriorCalculate posterior covariance and estimate parameters for...
held.out.posterior.by.variationOrder the genes by the variation of their posterior mean
held.out.posterior.filterFilter the genes
held.out.posterior.joinJoin with another data frame. Useful for adding gene names...
held.out.select.genesSelect held out genes by those with highest variance
inducing.covarianceCalculate the covariance structure of the inducing points
init.orderings.vs.pseudotimes.plotPlot the orderings for initialisation against the estimated...
is.de.loreanIs a DeLorean object?
knit.reportKnit a report, the file inst/Rmd/<report.name>.Rmd must exist...
kouno.exprKouno et al. investigated the transcriptional network...
make.fit.validMake a fit valid by running one iteration of the sampler.
make.init.fnReturns a function that constructs parameter settings with...
make.predictionsMake predictions
marg.like.plotPlot posterior for marginal log likelihoods of individual...
melt.exprMelt an expression matrix.
mutate.profile.dataMutate the profile data into shape compatible with GP plot...
optimise.best.sampleOptimise the best sample and update the best.sample index.
ordering.block.moveMove a block in an ordering and shift the other items.
ordering.improveImprove the ordering in the sense that some function is...
ordering.invertInvert the ordering
ordering.is.validCheck that it is a valid ordering
ordering.maximiseFind a good ordering in the sense that some function is...
ordering.metropolis.hastingsMetropolis-Hastings on orderings.
ordering.moveMove one item in an ordering and shift the other items.
ordering.random.block.moveRandomly move a block in an ordering to another location
ordering.random.moveRandomly move one item in an ordering to another location
orderings.plotPlot likelihoods of orderings against elapsed times taken to...
ordering.test.scoreTest ordering score: sum every time consecutive items are in...
partition.de.loreanPartition de.lorean object by cells
permute.dfPermute a data frame, x. If group.col is given it should name...
permuted.roughnessPermute cells and test roughness of expression.
plot.add.exprAdd expression data to a plot
plot.add.mean.and.varianceAdd posterior representation to a plot.
plot.de.loreanVarious DeLorean object plots
plot.held.out.posteriorPlot the posterior of held out genes
prepare.for.stanPrepare for Stan
print.de.loreanPrint details of DeLorean object
process.posteriorProcess the posterior, that is extract and reformat the...
profiles.plotPlot best sample predicted expression.
pseudotime.plotPlot pseudotime (tau) against observed capture time.
pseudotimes.from.orderingsConvert best orderings into initialisations
pseudotimes.pair.plotPlot two sets of pseudotimes against each other.
report.fileThe filename of the R markdown report.
Rhat.plotPlot the Rhat convergence statistics. 'examine.convergence'...
roughnesses.plotPlot results of roughness test
roughness.of.permutationsApply permutation based roughness test to held out genes
roughness.of.sampleCalculate the roughness of the held out genes given the...
roughness.testCalculate roughnesses under fit samples and also under random...
seriation.find.orderingsUse seriation package to find good orderings
tau.offsets.plotPlot the tau offsets, that is how much the pseudotimes (tau)...
test.fitTest fit for log normal and gamma
test.mhTest ordering Metropolis-Hastings sampler.
test.robustness.de.loreanTest robustness of pseudotime estimation on subsets of...
windram.exprWindram et al. investigated the defense response in...
JohnReid/DeLorean documentation built on July 28, 2017, 11:26 a.m.