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.

Install the latest version of this package by entering the following in R:
install.packages("DeLorean")
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...

Functions

adjust.by.cell.sizes Man page
alpha.for.rug Man page
analyse.noise.levels Man page
analyse.variance Man page
anders.huber.cell.sizes Man page
aov.dl Man page
avg.par.samples Man page
calc.inducing.pseudotimes Man page
calc.roughness Man page
centralise Man page
cmp.profiles.plot Man page
compile.model Man page
cov.all.genes.conditioned Man page
cov.calc.dists Man page
cov.calc.dl.dists Man page
cov.calc.gene Man page
cov.calc.gene.conditioned Man page
cov.matern.32 Man page
cov.periodise Man page
create.ordering.ll.fn Man page
default.num.cores Man page
de.lorean Man page
DeLorean Man page
DeLorean-package Man page
de.lorean.stylesheet Man page
dim.de.lorean Man page
estimate.cell.sizes Man page
estimate.hyper Man page
examine.convergence Man page
expected.sample.var Man page
expr.data.plot Man page
filter.cells Man page
filter.genes Man page
find.best.tau Man page
find.good.ordering Man page
find.smooth.tau Man page
fit.dl Man page
fit.held.out Man page
fit.model Man page
fit.model.sample Man page
fit.model.vb Man page
gaussian.condition Man page
gene.covariances Man page
get.posterior.mean Man page
gp.log.marg.like Man page
gp.predict Man page
gp.predictions.df Man page
guo.cell.meta Man page
guo.expr Man page
guo.gene.meta Man page
held.out.melt Man page
held.out.posterior Man page
held.out.posterior.by.variation Man page
held.out.posterior.filter Man page
held.out.posterior.join Man page
held.out.select.genes Man page
inducing.covariance Man page
init.orderings.vs.pseudotimes.plot Man page
is.de.lorean Man page
knit.report Man page
kouno.cell.meta Man page
kouno.expr Man page
kouno.gene.meta Man page
magda.find.orderings Man page
make.fit.valid Man page
make.init.fn Man page
make.predictions Man page
marg.like.plot Man page
melt.expr Man page
mutate.profile.data Man page
optimise.best.sample Man page
ordering.block.move Man page
ordering.improve Man page
ordering.invert Man page
ordering.is.valid Man page
ordering.maximise Man page
ordering.metropolis.hastings Man page
ordering.move Man page
ordering.random.block.move Man page
ordering.random.move Man page
orderings.plot Man page
ordering.test.score Man page
partition.de.lorean Man page
permute.df Man page
permuted.roughness Man page
plot.add.expr Man page
plot.add.mean.and.variance Man page
plot.de.lorean Man page
plot.held.out.posterior Man page
prepare.for.stan Man page
print.de.lorean Man page
process.posterior Man page
profiles.plot Man page
pseudotime.plot Man page
pseudotimes.from.orderings Man page
pseudotimes.pair.plot Man page
report.file Man page
Rhat.plot Man page
roughnesses.plot Man page
roughness.of.permutations Man page
roughness.of.sample Man page
roughness.test Man page
seriation.find.orderings Man page
tau.offsets.plot Man page
test.fit Man page
test.mh Man page
test.robustness.de.lorean Man page
windram.cell.meta Man page
windram.expr Man page
windram.gene.meta Man page

Files

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