DeLorean: Estimates Pseudotimes for Single Cell Expression Data

Implements the DeLorean model to estimate pseudotimes for single cell expression data. The DeLorean model uses a Gaussian process latent variable model to model uncertainty in the capture time of cross-sectional data.

AuthorJohn Reid <john.reid@mrc-bsu.cam.ac.uk>
Date of publication2016-10-05 14:37:34
MaintainerJohn Reid <john.reid@mrc-bsu.cam.ac.uk>
LicenseMIT + file LICENSE
Version1.2.4

View on CRAN

Man pages

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...

compile.model: Compile the model and cache the DSO to avoid unnecessary...

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: DeLorean.

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. - 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 Guassian on another. See Eqn. A.6 on page 200 of...

gene.covariances: Calculate the covariance structure of the tau

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...

magda.find.orderings: Use Magda's code to find good orderings

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...

Files in this package

DeLorean
DeLorean/inst
DeLorean/inst/scripts
DeLorean/inst/scripts/McDavid-fns.R
DeLorean/inst/scripts/Windram-DeLorean.Rmd
DeLorean/inst/scripts/complexity.Rmd
DeLorean/inst/scripts/test-smooth-tau.Rmd
DeLorean/inst/scripts/Trapnell-2014.md
DeLorean/inst/scripts/McDavid-Oscope.Rmd
DeLorean/inst/scripts/shared.R
DeLorean/inst/scripts/DeLorean.bib
DeLorean/inst/scripts/fetch-Windram.Rmd
DeLorean/inst/scripts/DeLorean-Trapnell.Rmd
DeLorean/inst/scripts/Windram-tau-posterior.eps
DeLorean/inst/scripts/Windram-Monocle-compare.eps
DeLorean/inst/scripts/parse-Kouno.Rmd
DeLorean/inst/scripts/Shalek-DeLorean.Rmd
DeLorean/inst/scripts/Tang-DeLorean.Rmd
DeLorean/inst/scripts/DeLorean-intro.Rnw
DeLorean/inst/scripts/fetch-Shalek-2014.Rmd
DeLorean/inst/scripts/DeLorean-model.Rmd
DeLorean/inst/scripts/config.R
DeLorean/inst/scripts/Windram-pseudotime-vs-obfuscated.eps
DeLorean/inst/scripts/DeLorean-inference.Rmd
DeLorean/inst/scripts/Tang-parse.Rmd
DeLorean/inst/scripts/McDavid-Monocle.Rmd
DeLorean/inst/scripts/Windram-make-plots.Rmd
DeLorean/inst/scripts/Windram-posterior-cor.eps
DeLorean/inst/scripts/DeLorean-Guo.Rmd
DeLorean/inst/scripts/McDavid-DeLorean.Rmd
DeLorean/inst/scripts/Guo-rand-proj.Rmd
DeLorean/inst/scripts/Kouno-DeLorean.Rmd
DeLorean/inst/scripts/Windram-Monocle.Rmd
DeLorean/inst/scripts/Trapnell-2014.Rmd
DeLorean/inst/Rmd
DeLorean/inst/Rmd/profiles.Rmd
DeLorean/inst/Rmd/data.Rmd
DeLorean/inst/Rmd/foghorn.css
DeLorean/inst/Rmd/cellsizes.Rmd
DeLorean/inst/Rmd/convergence.Rmd
DeLorean/inst/Rmd/hyper-parameters.Rmd
DeLorean/inst/Rmd/posterior.Rmd
DeLorean/inst/Stan
DeLorean/inst/Stan/exact-sizes.stan
DeLorean/inst/Stan/lowrank-sizes.stan
DeLorean/inst/Stan/exact.stan
DeLorean/inst/Stan/lowrank.stan
DeLorean/inst/extdata
DeLorean/inst/extdata/Shalek-2014-Supp-Table-2.csv
DeLorean/inst/extdata/gb-2013-14-10-r118-s3.csv
DeLorean/inst/extdata/Shalek-2014-Supp-Table-3.csv
DeLorean/inst/doc
DeLorean/inst/doc/Test_vignette.Rmd
DeLorean/inst/doc/DeLorean.Rmd
DeLorean/inst/doc/DeLorean.html
DeLorean/inst/doc/DeLorean.R
DeLorean/inst/doc/Test_vignette.R
DeLorean/inst/doc/Test_vignette.html
DeLorean/tests
DeLorean/tests/testthat.R
DeLorean/tests/testthat
DeLorean/tests/testthat/test-guo.r
DeLorean/NAMESPACE
DeLorean/NEWS.md
DeLorean/data
DeLorean/data/WindramDeLorean.rda
DeLorean/data/GuoDeLorean.rda
DeLorean/data/KounoDeLorean.rda
DeLorean/R
DeLorean/R/report.r
DeLorean/R/cell-size.r
DeLorean/R/plot.r
DeLorean/R/package.r
DeLorean/R/magda.r
DeLorean/R/model.r
DeLorean/R/ordering.r
DeLorean/R/held-out.r
DeLorean/R/aov.r
DeLorean/R/gp.r
DeLorean/R/robustness.r
DeLorean/R/smoothness.r
DeLorean/R/data.r
DeLorean/vignettes
DeLorean/vignettes/DeLorean.Rmd
DeLorean/README.md
DeLorean/MD5
DeLorean/build
DeLorean/build/vignette.rds
DeLorean/DESCRIPTION
DeLorean/man
DeLorean/man/analyse.noise.levels.Rd DeLorean/man/fit.model.sample.Rd DeLorean/man/cov.calc.dists.Rd DeLorean/man/guo.expr.Rd DeLorean/man/ordering.random.block.move.Rd DeLorean/man/profiles.plot.Rd DeLorean/man/gene.covariances.Rd DeLorean/man/tau.offsets.plot.Rd DeLorean/man/ordering.improve.Rd DeLorean/man/knit.report.Rd DeLorean/man/held.out.posterior.by.variation.Rd DeLorean/man/kouno.expr.Rd DeLorean/man/centralise.Rd DeLorean/man/expected.sample.var.Rd DeLorean/man/held.out.posterior.Rd DeLorean/man/calc.inducing.pseudotimes.Rd DeLorean/man/held.out.select.genes.Rd DeLorean/man/plot.de.lorean.Rd DeLorean/man/gp.predictions.df.Rd DeLorean/man/cmp.profiles.plot.Rd DeLorean/man/inducing.covariance.Rd DeLorean/man/cov.matern.32.Rd DeLorean/man/DeLorean.Rd DeLorean/man/find.best.tau.Rd DeLorean/man/ordering.block.move.Rd DeLorean/man/get.posterior.mean.Rd DeLorean/man/make.fit.valid.Rd DeLorean/man/is.de.lorean.Rd DeLorean/man/process.posterior.Rd DeLorean/man/pseudotimes.pair.plot.Rd DeLorean/man/seriation.find.orderings.Rd DeLorean/man/held.out.melt.Rd DeLorean/man/Rhat.plot.Rd DeLorean/man/partition.de.lorean.Rd DeLorean/man/make.predictions.Rd DeLorean/man/default.num.cores.Rd DeLorean/man/compile.model.Rd DeLorean/man/plot.held.out.posterior.Rd DeLorean/man/estimate.cell.sizes.Rd DeLorean/man/ordering.maximise.Rd DeLorean/man/alpha.for.rug.Rd DeLorean/man/de.lorean.stylesheet.Rd DeLorean/man/gp.log.marg.like.Rd DeLorean/man/fit.model.Rd DeLorean/man/examine.convergence.Rd DeLorean/man/anders.huber.cell.sizes.Rd DeLorean/man/ordering.is.valid.Rd DeLorean/man/init.orderings.vs.pseudotimes.plot.Rd DeLorean/man/plot.add.mean.and.variance.Rd DeLorean/man/roughness.of.permutations.Rd DeLorean/man/estimate.hyper.Rd DeLorean/man/ordering.test.score.Rd DeLorean/man/expr.data.plot.Rd DeLorean/man/filter.cells.Rd DeLorean/man/avg.par.samples.Rd DeLorean/man/ordering.move.Rd DeLorean/man/aov.dl.Rd DeLorean/man/held.out.posterior.join.Rd DeLorean/man/orderings.plot.Rd DeLorean/man/cov.periodise.Rd DeLorean/man/prepare.for.stan.Rd DeLorean/man/de.lorean.Rd DeLorean/man/magda.find.orderings.Rd DeLorean/man/melt.expr.Rd DeLorean/man/dim.de.lorean.Rd DeLorean/man/test.fit.Rd DeLorean/man/optimise.best.sample.Rd DeLorean/man/pseudotimes.from.orderings.Rd DeLorean/man/roughness.of.sample.Rd DeLorean/man/held.out.posterior.filter.Rd DeLorean/man/find.good.ordering.Rd DeLorean/man/test.mh.Rd DeLorean/man/make.init.fn.Rd DeLorean/man/marg.like.plot.Rd DeLorean/man/fit.model.vb.Rd DeLorean/man/fit.dl.Rd DeLorean/man/windram.expr.Rd DeLorean/man/cov.calc.gene.Rd DeLorean/man/pseudotime.plot.Rd DeLorean/man/cov.calc.dl.dists.Rd DeLorean/man/ordering.metropolis.hastings.Rd DeLorean/man/ordering.invert.Rd DeLorean/man/fit.held.out.Rd DeLorean/man/gp.predict.Rd DeLorean/man/cov.calc.gene.conditioned.Rd DeLorean/man/report.file.Rd DeLorean/man/permuted.roughness.Rd DeLorean/man/roughnesses.plot.Rd DeLorean/man/analyse.variance.Rd DeLorean/man/print.de.lorean.Rd DeLorean/man/filter.genes.Rd DeLorean/man/find.smooth.tau.Rd DeLorean/man/adjust.by.cell.sizes.Rd DeLorean/man/mutate.profile.data.Rd DeLorean/man/plot.add.expr.Rd DeLorean/man/permute.df.Rd DeLorean/man/test.robustness.de.lorean.Rd DeLorean/man/roughness.test.Rd DeLorean/man/calc.roughness.Rd DeLorean/man/ordering.random.move.Rd DeLorean/man/cov.all.genes.conditioned.Rd DeLorean/man/gaussian.condition.Rd DeLorean/man/create.ordering.ll.fn.Rd
DeLorean/LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.