stochprofML: Stochastic Profiling using Maximum Likelihood Estimation

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This is an R package accompanying the paper "Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles" by Sameer S Bajikar, Christiane Fuchs, Andreas Roller, Fabian J Theis and Kevin A Janes (PNAS 2014, 111(5), E626-635). In this paper, we measure expression profiles from small heterogeneous populations of cells, where each cell is assumed to be from a mixture of lognormal distributions. We perform maximum likelihood estimation in order to infer the mixture ratio and the parameters of these lognormal distributions from the cumulated expression measurements.

Author
Christiane Fuchs
Date of publication
2014-10-18 06:28:46
Maintainer
Christiane Fuchs <christiane.fuchs@helmholtz-muenchen.de>
License
GPL (>= 2)
Version
1.2

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Man pages

analyze.sod2
Analysis of SOD2 data in stochastic profiling model
analyze.toycluster
Analysis of toyclusters in stochastic profiling model
calculate.ci.EXPLN
Maximum likelihood confidence intervals for EXP-LN model
calculate.ci.LNLN
Maximum likelihood confidence intervals for LN-LN model
calculate.ci.rLNLN
Maximum likelihood confidence intervals for rLN-LN model
comb.summands
Combinations of fixed number of summands with pre-defined...
d.sum.of.mixtures.EXPLN
Sums of mixtures of zero, one or more lognormal random...
d.sum.of.mixtures.LNLN
Sums of mixtures of lognormal random variables
d.sum.of.mixtures.rLNLN
Sums of mixtures of lognormal random variables
generate.toydata
Generation and analysis of synthetic data in stochastic...
penalty.constraint.EXPLN
Penalization for population densities that do not fulfil...
penalty.constraint.LNLN
Penalization for population densities that do not fulfil...
penalty.constraint.rLNLN
Penalization for population densities that do not fulfil...
sod2
Measurements from the detoxifying enzyme, SOD2
stochasticProfilingData
User prompt for generation and visualization of synthetic...
stochasticProfilingML
User prompt for maximum likelihood estimation of stochastic...
stochprof.loop
Maximum likelihood estimation for the parameters in the...
stochprofML-package
Stochastic Profiling using Maximum Likelihood Estimation
stochprof.results.EXPLN
Evaluation of results from estimation of EXP-LN model
stochprof.results.LNLN
Evaluation of results from estimation of LN-LN model
stochprof.results.rLNLN
Evaluation of results from estimation of rLN-LN model
stochprof.search.EXPLN
Calculation of the log likelihood function of the EXP-LN...
stochprof.search.LNLN
Calculation of the log likelihood function of the LN-LN model
stochprof.search.rLNLN
Calculation of the log likelihood function of the rLN-LN...
toycluster.EXPLN
Synthetic data from the EXP-LN model
toycluster.LNLN
Synthetic data from the LN-LN model
toycluster.rLNLN
Synthetic data from the rLN-LN model

Files in this package

stochprofML
stochprofML/NAMESPACE
stochprofML/data
stochprofML/data/sod2.rda
stochprofML/data/toycluster.EXPLN.rda
stochprofML/data/toycluster.LNLN.rda
stochprofML/data/toycluster.rLNLN.rda
stochprofML/R
stochprofML/R/stochprof.logit.R
stochprofML/R/d.sum.of.types.rLNLN.R
stochprofML/R/stochprof.search.LNLN.R
stochprofML/R/d.sum.of.types.LNLN.R
stochprofML/R/r.sum.of.mixtures.EXPLN.R
stochprofML/R/lognormal.exp.convolution.R
stochprofML/R/get.range.rLNLN.R
stochprofML/R/d.sum.of.mixtures.EXPLN.R
stochprofML/R/calculate.ci.rLNLN.R
stochprofML/R/comb.summands.R
stochprofML/R/get.range.EXPLN.R
stochprofML/R/r.sum.of.mixtures.LNLN.R
stochprofML/R/generate.toydata.R
stochprofML/R/stochasticProfilingML.R
stochprofML/R/penalty.constraint.EXPLN.R
stochprofML/R/r.sum.of.mixtures.rLNLN.R
stochprofML/R/d.sum.of.mixtures.rLNLN.R
stochprofML/R/analyze.sod2.R
stochprofML/R/stochprof.results.EXPLN.R
stochprofML/R/d.sum.of.lognormal.types.R
stochprofML/R/stochprof.expit.R
stochprofML/R/draw.parameters.rLNLN.R
stochprofML/R/d.sum.of.lognormals.R
stochprofML/R/calculate.ci.EXPLN.R
stochprofML/R/stochprof.loop.R
stochprofML/R/stochprof.results.rLNLN.R
stochprofML/R/stochprof.results.LNLN.R
stochprofML/R/transform.par.EXPLN.R
stochprofML/R/draw.parameters.EXPLN.R
stochprofML/R/backtransform.par.EXPLN.R
stochprofML/R/get.range.LNLN.R
stochprofML/R/penalty.constraint.LNLN.R
stochprofML/R/d.sum.of.exp.types.R
stochprofML/R/transform.par.rLNLN.R
stochprofML/R/stochprof.search.EXPLN.R
stochprofML/R/analyze.toycluster.R
stochprofML/R/stochprof.search.rLNLN.R
stochprofML/R/stochasticProfilingData.R
stochprofML/R/transform.par.LNLN.R
stochprofML/R/backtransform.par.rLNLN.R
stochprofML/R/d.sum.of.mixtures.LNLN.R
stochprofML/R/penalty.constraint.rLNLN.R
stochprofML/R/set.model.functions.R
stochprofML/R/calculate.ci.LNLN.R
stochprofML/R/backtransform.par.LNLN.R
stochprofML/R/draw.parameters.LNLN.R
stochprofML/R/stochprofML-internal.R
stochprofML/MD5
stochprofML/DESCRIPTION
stochprofML/man
stochprofML/man/stochasticProfilingData.Rd
stochprofML/man/calculate.ci.EXPLN.Rd
stochprofML/man/toycluster.LNLN.Rd
stochprofML/man/generate.toydata.Rd
stochprofML/man/calculate.ci.rLNLN.Rd
stochprofML/man/stochprof.results.EXPLN.Rd
stochprofML/man/calculate.ci.LNLN.Rd
stochprofML/man/stochprofML-package.Rd
stochprofML/man/penalty.constraint.EXPLN.Rd
stochprofML/man/stochasticProfilingML.Rd
stochprofML/man/stochprof.search.EXPLN.Rd
stochprofML/man/toycluster.EXPLN.Rd
stochprofML/man/penalty.constraint.LNLN.Rd
stochprofML/man/d.sum.of.mixtures.EXPLN.Rd
stochprofML/man/d.sum.of.mixtures.LNLN.Rd
stochprofML/man/toycluster.rLNLN.Rd
stochprofML/man/stochprof.results.LNLN.Rd
stochprofML/man/stochprof.search.rLNLN.Rd
stochprofML/man/comb.summands.Rd
stochprofML/man/analyze.sod2.Rd
stochprofML/man/stochprof.loop.Rd
stochprofML/man/d.sum.of.mixtures.rLNLN.Rd
stochprofML/man/penalty.constraint.rLNLN.Rd
stochprofML/man/analyze.toycluster.Rd
stochprofML/man/stochprof.results.rLNLN.Rd
stochprofML/man/sod2.Rd
stochprofML/man/stochprof.search.LNLN.Rd