An R package for the Bayesian analysis of differential
subcellular localisation experiments
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Documentation for package ‘bandle’ version 1.11.0
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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 |
| 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 |