DeLorean: Estimates Pseudotimes for Single Cell Expression Data

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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.

Author
John Reid <john.reid@mrc-bsu.cam.ac.uk>
Date of publication
2016-10-05 14:37:34
Maintainer
John Reid <john.reid@mrc-bsu.cam.ac.uk>
License
MIT + file LICENSE
Version
1.2.4

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