stochprofML: Stochastic Profiling using Maximum Likelihood Estimation
Version 1.2

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.

AuthorChristiane Fuchs
Date of publication2014-10-18 06:28:46
MaintainerChristiane Fuchs <christiane.fuchs@helmholtz-muenchen.de>
LicenseGPL (>= 2)
Version1.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("stochprofML")

Getting started

Package overview

Popular man pages

analyze.toycluster: Analysis of toyclusters in stochastic profiling model
d.sum.of.mixtures.rLNLN: Sums of mixtures of lognormal random variables
penalty.constraint.EXPLN: Penalization for population densities that do not fulfil...
penalty.constraint.rLNLN: Penalization for population densities that do not fulfil...
stochasticProfilingData: User prompt for generation and visualization of synthetic...
stochprofML-package: Stochastic Profiling using Maximum Likelihood Estimation
stochprof.results.rLNLN: Evaluation of results from estimation of rLN-LN model
See all...

All man pages Function index File listing

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

Functions

analyze.sod2 Man page Source code
analyze.toycluster Man page Source code
backtransform.par.EXPLN Source code
backtransform.par.LNLN Source code
backtransform.par.rLNLN Source code
calculate.ci.EXPLN Man page Source code
calculate.ci.LNLN Man page Source code
calculate.ci.rLNLN Man page Source code
comb.summands Man page Source code
d.sum.of.exp.types Source code
d.sum.of.lognormal.types Source code
d.sum.of.lognormals Source code
d.sum.of.mixtures.EXPLN Man page Source code
d.sum.of.mixtures.LNLN Man page Source code
d.sum.of.mixtures.rLNLN Man page Source code
d.sum.of.types.LNLN Source code
d.sum.of.types.rLNLN Source code
draw.parameters.EXPLN Source code
draw.parameters.LNLN Source code
draw.parameters.rLNLN Source code
generate.toydata Man page Source code
get.range.EXPLN Source code
get.range.LNLN Source code
get.range.rLNLN Source code
lognormal.exp.convolution Source code
penalty.constraint.EXPLN Man page Source code
penalty.constraint.LNLN Man page Source code
penalty.constraint.rLNLN Man page Source code
r.sum.of.mixtures.EXPLN Man page Source code
r.sum.of.mixtures.LNLN Man page Source code
r.sum.of.mixtures.rLNLN Man page Source code
set.model.functions Source code
sod2 Man page
stochasticProfilingData Man page Source code
stochasticProfilingML Man page Source code
stochprof.expit Source code
stochprof.logit Source code
stochprof.loop Man page Source code
stochprof.results.EXPLN Man page Source code
stochprof.results.LNLN Man page Source code
stochprof.results.rLNLN Man page Source code
stochprof.search.EXPLN Man page Source code
stochprof.search.LNLN Man page Source code
stochprof.search.rLNLN Man page Source code
stochprofML Man page
stochprofML-package Man page
toycluster.EXPLN Man page
toycluster.LNLN Man page
toycluster.rLNLN Man page
transform.par.EXPLN Source code
transform.par.LNLN Source code
transform.par.rLNLN Source code

Files

NAMESPACE
data
data/sod2.rda
data/toycluster.EXPLN.rda
data/toycluster.LNLN.rda
data/toycluster.rLNLN.rda
R
R/stochprof.logit.R
R/d.sum.of.types.rLNLN.R
R/stochprof.search.LNLN.R
R/d.sum.of.types.LNLN.R
R/r.sum.of.mixtures.EXPLN.R
R/lognormal.exp.convolution.R
R/get.range.rLNLN.R
R/d.sum.of.mixtures.EXPLN.R
R/calculate.ci.rLNLN.R
R/comb.summands.R
R/get.range.EXPLN.R
R/r.sum.of.mixtures.LNLN.R
R/generate.toydata.R
R/stochasticProfilingML.R
R/penalty.constraint.EXPLN.R
R/r.sum.of.mixtures.rLNLN.R
R/d.sum.of.mixtures.rLNLN.R
R/analyze.sod2.R
R/stochprof.results.EXPLN.R
R/d.sum.of.lognormal.types.R
R/stochprof.expit.R
R/draw.parameters.rLNLN.R
R/d.sum.of.lognormals.R
R/calculate.ci.EXPLN.R
R/stochprof.loop.R
R/stochprof.results.rLNLN.R
R/stochprof.results.LNLN.R
R/transform.par.EXPLN.R
R/draw.parameters.EXPLN.R
R/backtransform.par.EXPLN.R
R/get.range.LNLN.R
R/penalty.constraint.LNLN.R
R/d.sum.of.exp.types.R
R/transform.par.rLNLN.R
R/stochprof.search.EXPLN.R
R/analyze.toycluster.R
R/stochprof.search.rLNLN.R
R/stochasticProfilingData.R
R/transform.par.LNLN.R
R/backtransform.par.rLNLN.R
R/d.sum.of.mixtures.LNLN.R
R/penalty.constraint.rLNLN.R
R/set.model.functions.R
R/calculate.ci.LNLN.R
R/backtransform.par.LNLN.R
R/draw.parameters.LNLN.R
R/stochprofML-internal.R
MD5
DESCRIPTION
man
man/stochasticProfilingData.Rd
man/calculate.ci.EXPLN.Rd
man/toycluster.LNLN.Rd
man/generate.toydata.Rd
man/calculate.ci.rLNLN.Rd
man/stochprof.results.EXPLN.Rd
man/calculate.ci.LNLN.Rd
man/stochprofML-package.Rd
man/penalty.constraint.EXPLN.Rd
man/stochasticProfilingML.Rd
man/stochprof.search.EXPLN.Rd
man/toycluster.EXPLN.Rd
man/penalty.constraint.LNLN.Rd
man/d.sum.of.mixtures.EXPLN.Rd
man/d.sum.of.mixtures.LNLN.Rd
man/toycluster.rLNLN.Rd
man/stochprof.results.LNLN.Rd
man/stochprof.search.rLNLN.Rd
man/comb.summands.Rd
man/analyze.sod2.Rd
man/stochprof.loop.Rd
man/d.sum.of.mixtures.rLNLN.Rd
man/penalty.constraint.rLNLN.Rd
man/analyze.toycluster.Rd
man/stochprof.results.rLNLN.Rd
man/sod2.Rd
man/stochprof.search.LNLN.Rd
stochprofML documentation built on May 20, 2017, 12:05 a.m.

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