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

## Documentation for package ‘bandle’ version 1.16.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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
bandle_get_outliers | Number of outliers at each iteration of MCMC
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 --

calculateGelman | Calculate the Gelman and Rubin diagnostic for bandle output
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
plotOutliers | Generate trace and density plots for all chains
plotTable | Generate a table of differential localisations
plotTranslocations | Plot 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