Man pages for JohnReid/DeLorean
Estimates Pseudotimes for Single Cell Expression Data
| adjust.by.cell.sizes | Adjust the expression by the estimated cell sizes. |
| alpha.for.rug | Calculate a suitable value for a rug plot given the number of... |
| analyse.noise.levels | Analyse noise levels and assess which genes have the greatest... |
| analyse.variance | Analyse variance of expression between and within capture... |
| anders.huber.cell.sizes | Estimate the cell sizes according to Anders & Huber... |
| aov.dl | Perform an analysis of variance to select genes for the... |
| avg.par.samples | Average across a parameters samples. |
| calc.inducing.pseudotimes | Calculate inducing pseudotimes for sparse approximation |
| calc.roughness | Calculate the roughness of the vector. The roughness is the... |
| centralise | Centralises a periodic position into [period/2, period) by... |
| cmp.profiles.plot | Plot a comparison of the profiles from several de.lorean... |
| cov.all.genes.conditioned | Calculate covariances for all genes when conditioned on data... |
| cov.calc.dists | Calculate distances between vectors of time points |
| cov.calc.dl.dists | Calculate distances over estimated pseudotimes and test... |
| cov.calc.gene | Calculate covariance structure for gene over pseudotimes and... |
| cov.calc.gene.conditioned | Calculate covariance for gene over test inputs when... |
| cov.matern.32 | Matern 3/2 covariance function |
| cov.periodise | Makes a distance periodic |
| create.ordering.ll.fn | Calculate the covariance structure of evenly spread tau and... |
| default.num.cores | Default number of cores to use. |
| de.lorean | Initialise DeLorean object |
| DeLorean-package | The 'DeLorean' package. |
| de.lorean.stylesheet | The filename of the R markdown stylesheet |
| dim.de.lorean | Dimensions of DeLorean object |
| estimate.cell.sizes | Estimate the cell sizes. We only consider genes that are... |
| estimate.hyper | Estimate hyperparameters for model using empirical Bayes. |
| examine.convergence | Analyse the samples and gather the convergence statistics.... |
| expected.sample.var | The expected within sample variance of a Gaussian with the... |
| expr.data.plot | Plot the expression data by the capture points |
| filter_cells | Filter cells |
| filter_genes | Filter genes |
| find.best.tau | Find best tau to initialise chains with by sampling tau from... |
| find.good.ordering | Run a find good ordering method and append results to... |
| find.smooth.tau | Find best order of the samples assuming some smooth GP prior... |
| fit.dl | Perform all the steps necessary to fit the model: 1. prepare... |
| fit.held.out | Fit held out genes |
| fit.model | Fit the model using specified method (sampling or variational... |
| fit.model.sample | Fit the model using Stan sampler |
| fit.model.vb | Fit the model using Stan variational Bayes |
| gaussian.condition | Condition a Gaussian on another. See Eqn. A.6 on page 200 of... |
| gene.covariances | Calculate the covariance structure of the tau |
| get_model | Get the Stan model for a DeLorean object. |
| get.posterior.mean | Get posterior mean of samples |
| gp.log.marg.like | The log marginal likelihood. See "2.3 Varying the... |
| gp.predict | Predictive mean, variance and log marginal likelihood of a... |
| gp.predictions.df | Convert the output of gp.predict() into a data.frame. |
| guo.expr | Single cell expression data and meta data from Guo et al.... |
| held.out.melt | Melt held out genes |
| held.out.posterior | Calculate posterior covariance and estimate parameters for... |
| held.out.posterior.by.variation | Order the genes by the variation of their posterior mean |
| held.out.posterior.filter | Filter the genes |
| held.out.posterior.join | Join with another data frame. Useful for adding gene names... |
| held.out.select.genes | Select held out genes by those with highest variance |
| inducing.covariance | Calculate the covariance structure of the inducing points |
| init.orderings.vs.pseudotimes.plot | Plot the orderings for initialisation against the estimated... |
| is.de.lorean | Is a DeLorean object? |
| knit.report | Knit a report, the file inst/Rmd/<report.name>.Rmd must exist... |
| kouno.expr | Kouno et al. investigated the transcriptional network... |
| make.fit.valid | Make a fit valid by running one iteration of the sampler. |
| make.init.fn | Returns a function that constructs parameter settings with... |
| make.predictions | Make predictions |
| marg.like.plot | Plot posterior for marginal log likelihoods of individual... |
| melt.expr | Melt an expression matrix. |
| mutate.profile.data | Mutate the profile data into shape compatible with GP plot... |
| optimise.best.sample | Optimise the best sample and update the best.sample index. |
| ordering.block.move | Move a block in an ordering and shift the other items. |
| ordering.improve | Improve the ordering in the sense that some function is... |
| ordering.invert | Invert the ordering |
| ordering.is.valid | Check that it is a valid ordering |
| ordering.maximise | Find a good ordering in the sense that some function is... |
| ordering.metropolis.hastings | Metropolis-Hastings on orderings. |
| ordering.move | Move one item in an ordering and shift the other items. |
| ordering.random.block.move | Randomly move a block in an ordering to another location |
| ordering.random.move | Randomly move one item in an ordering to another location |
| orderings.plot | Plot likelihoods of orderings against elapsed times taken to... |
| ordering.test.score | Test ordering score: sum every time consecutive items are in... |
| partition.de.lorean | Partition de.lorean object by cells |
| permute.df | Permute a data frame, x. If group.col is given it should name... |
| permuted.roughness | Permute cells and test roughness of expression. |
| plot.add.expr | Add expression data to a plot |
| plot.add.mean.and.variance | Add posterior representation to a plot. |
| plot.de.lorean | Various DeLorean object plots |
| plot.held.out.posterior | Plot the posterior of held out genes |
| prepare.for.stan | Prepare for Stan |
| print.de.lorean | Print details of DeLorean object |
| process.posterior | Process the posterior, that is extract and reformat the... |
| profiles.plot | Plot best sample predicted expression. |
| pseudotime.plot | Plot pseudotime (tau) against observed capture time. |
| pseudotimes.from.orderings | Convert best orderings into initialisations |
| pseudotimes.pair.plot | Plot two sets of pseudotimes against each other. |
| report.file | The filename of the R markdown report. |
| Rhat.plot | Plot the Rhat convergence statistics. 'examine.convergence'... |
| roughnesses.plot | Plot results of roughness test |
| roughness.of.permutations | Apply permutation based roughness test to held out genes |
| roughness.of.sample | Calculate the roughness of the held out genes given the... |
| roughness.test | Calculate roughnesses under fit samples and also under random... |
| seriation.find.orderings | Use seriation package to find good orderings |
| tau.offsets.plot | Plot the tau offsets, that is how much the pseudotimes (tau)... |
| test.fit | Test fit for log normal and gamma |
| test.mh | Test ordering Metropolis-Hastings sampler. |
| test.robustness.de.lorean | Test robustness of pseudotime estimation on subsets of... |
| windram.expr | Windram et al. investigated the defense response in... |
