An R package for the Bayesian analysis of differential subcellular localisation experiments


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Documentation for package ‘bandle’ version 1.6.0

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B C D E F G K L M N O P R S T misc

bandle-package An R package for the Bayesian analysis of differential subcellular localisation experiments

-- B --

bandle Differential localisation experiments using the bandle method
bandleChain-class Infrastructure to to store and process MCMC results
bandleChains-class Infrastructure to to store and process MCMC results
bandleJoint Infrastructure to to store and process MCMC results
bandleJoint-method Infrastructure to to store and process MCMC results
bandleParams-class Infrastructure to to store and process MCMC results
bandlePredict Make predictions from a bandle analysis
bandleProcess process bandle results
bandleSummaries-class Infrastructure to to store and process MCMC results
bandleSummary-class Infrastructure to to store and process MCMC results
besselK bessel function of the second kind from boost library
besselK_boost bessel function of the second kind from boost library
binomialDiffLocProb Compute differential localisation probabilities from ms-based experiments using the bandle method
bootstrapdiffLocprob Compute differential localisation probabilities from ms-based experiments using the bandle method

-- C --

centeredData bessel function of the second kind from boost library
centeredDatamatern bessel function of the second kind from boost library
chains Infrastructure to to store and process MCMC results
comploglike bessel function of the second kind from boost library
comploglikelist bessel function of the second kind from boost library
componentloglike bessel function of the second kind from boost library
covOrganelle sample allocations, probabilities and compute loglikilihoods

-- D --

diffLoc Differential localisation experiments using the bandle method
diffLocalisationProb Compute differential localisation probabilities from ms-based experiments using the bandle method
dmvtCpp bessel function of the second kind from boost library
dmvtInt bessel function of the second kind from boost library

-- E --

EFDR Compute the expected False Discovery Rate

-- F --

fitGP Fit a Gaussian process to spatial proteomics data
fitGPmatern Fit a Gaussian process to spatial proteomics data
fitGPmaternPC Fit a Gaussian process to spatial proteomics data

-- G --

gpParams-class Container for GP results
gradientamatern bessel function of the second kind from boost library
gradientGP Compute GP gradient
gradientGPcpp bessel function of the second kind from boost library
gradientGPcppmatern bessel function of the second kind from boost library
gradientGPmatern Compute GP gradient
gradientlogprior Compute GP gradient
gradientrhomatern bessel function of the second kind from boost library
Gumbel Compute GP gradient

-- K --

kldir Computes the Kullback-Leibler divergence between Polya-Gamma and Dirichlet priors
kldirpg Computes the Kullback-Leibler divergence between Polya-Gamma and Dirichlet priors

-- L --

LeapfrogGPcpp bessel function of the second kind from boost library
LeapfrogGPcppPC bessel function of the second kind from boost library
length-method Infrastructure to to store and process MCMC results
likelihoodGP Compute GP gradient
likelihoodGPcpp bessel function of the second kind from boost library
likelihoodGPmatern Compute GP gradient
loglikeGPcpp bessel function of the second kind from boost library

-- M --

mahaInt bessel function of the second kind from boost library
makeComponent bessel function of the second kind from boost library
matern bessel function of the second kind from boost library
mcmc_plot_probs Generate a violin plot showing the probabilitiy of protein localisation to different organelles
meanOrganelle Computes Organelle means and variances using markers
metropolisGP Compute GP gradient
metropolisGPmatern Compute GP gradient
mrMethod robust Mahalanobis distance

-- N --

nicheParam-class Infrastructure to to store and process MCMC results
nicheParams-class Infrastructure to to store and process MCMC results
normalisedData bessel function of the second kind from boost library
normalisedDatamatern bessel function of the second kind from boost library

-- O --

outlierAllocationProbs sample allocations, probabilities and compute loglikilihoods

-- P --

params Infrastructure to to store and process MCMC results
PCrhomvar Compute GP gradient
pg_prior sample allocations, probabilities and compute loglikilihoods
plotConvergence Generates a histogram of ranks (a rank plot) for convergence
plotGPmatern Fit a Gaussian process to spatial proteomics data
plotTable Generates a table for visualising changes in localisation between two conditions/datasets
plotTranslocations Generates a chord diagram or alluvial plot for visualising changes in localisation between two conditions/datasets
posteriorEstimates Infrastructure to to store and process MCMC results
posteriorEstimates-method Infrastructure to to store and process MCMC results
posteriorGPmatern Compute GP gradient
posteriorgradientGPmatern Compute GP gradient
prior_pred_dir Computes the Kullback-Leibler divergence between Polya-Gamma and Dirichlet priors
prior_pred_pg Computes the Kullback-Leibler divergence between Polya-Gamma and Dirichlet priors
proteinAllocation sample allocations, probabilities and compute loglikilihoods

-- R --

rcpp_pgdraw bessel function of the second kind from boost library
reprodScore robust Mahalanobis distance
robustMahalanobis robust Mahalanobis distance

-- S --

sampleAlloccpp bessel function of the second kind from boost library
sampleDirichlet bessel function of the second kind from boost library
sampleGPmeancpp bessel function of the second kind from boost library
sampleGPmeanmaterncpp bessel function of the second kind from boost library
sampleOutlier sample allocations, probabilities and compute loglikilihoods
sampleOutliercpp bessel function of the second kind from boost library
sample_weights_dir sample allocations, probabilities and compute loglikilihoods
sample_weights_pg sample allocations, probabilities and compute loglikilihoods
show-method Infrastructure to to store and process MCMC results
sim_dynamic Generate a dynamic spatial proteomics experiment
spatial2D Generate a PCA plot with smoothed probability contours
StatStratum inherits StatSratum
summaries Infrastructure to to store and process MCMC results

-- T --

trenchDetcpp bessel function of the second kind from boost library
trenchInvcpp bessel function of the second kind from boost library

-- misc --

.bandleChain Infrastructure to to store and process MCMC results
.bandleChains Infrastructure to to store and process MCMC results
.bandleParams Infrastructure to to store and process MCMC results
.bandleSummaries Infrastructure to to store and process MCMC results
.bandleSummary Infrastructure to to store and process MCMC results
.gpParams Container for GP results
.nicheParam Infrastructure to to store and process MCMC results
.nicheParams Infrastructure to to store and process MCMC results
[-method Infrastructure to to store and process MCMC results
[[-method Infrastructure to to store and process MCMC results