Introduction | Installation | The data | A well-defined theoretical example | Preparing for bandle analysis | Fitting Gaussian processes | Setting the prior on the weights | Running the bandle function | Analysing bandle output | Assesing the model for convergence | Removing unconverged chains | Populating a bandleres object | Predicting the subcellular location | Thresholding on protein allocations | Distribution on allocations | Proteins assigned to one main location | Proteins with uncertainty | Differential localisation probability | Visualising differential localisation | Additional analysis | Estimating uncertainty in differential localisation | The bootstrapdiffLocprob function | The binomDiffLoc function | Obtaining probability estimates | The expected false discovery rate | Description of bandle parameters | Session information | References
Package: bandle 1.17.0
Oliver M. Crook
bandle: An R package for the Bayesian analysis of differential subcellular localisation experiments
The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.
Authors:
bandle_1.17.0.tar.gz
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bandle_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
bandle/json (API)
| # Install 'bandle' in R: |
| install.packages('bandle', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ococrook/bandle/issues
Uses libs:
On BioConductor:bandle-1.17.0(bioc 3.24)bandle-1.16.0(bioc 3.23)
bayesianclassificationclusteringimmunooncologyqualitycontroldataimportproteomicsmassspectrometryopenblascppopenmp
Last updated from:e1803fe866. Checks:12 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 327 | ||
| linux-devel-arm64 | WARNING | 600 | ||
| linux-devel-x86_64 | WARNING | 709 | ||
| source / vignettes | OK | 544 | ||
| linux-release-arm64 | WARNING | 592 | ||
| linux-release-x86_64 | WARNING | 691 | ||
| macos-release-arm64 | WARNING | 375 | ||
| macos-release-x86_64 | WARNING | 748 | ||
| macos-oldrel-arm64 | WARNING | 326 | ||
| macos-oldrel-x86_64 | WARNING | 841 | ||
| windows-devel | WARNING | 688 | ||
| windows-release | WARNING | 719 | ||
| windows-oldrel | WARNING | 648 | ||
| wasm-release | OK | 300 |
Exports:bandlebandle_get_outliersbandleJointbandlePredictbandleProcessbinomialDiffLocProbbootstrapdiffLocprobcalculateGelmancovOrganellediffLocdiffLocalisationProbdmvtCppEFDRfitGPfitGPmaternfitGPmaternPCGumbelkldirkldirpgmcmc_plot_probsmeanOrganellemrMethodpg_priorplotConvergenceplotGPmaternplotOutliersplotTableplotTranslocationsposteriorEstimatesprior_pred_dirprior_pred_pgsim_dynamicspatial2DStatStratumsummaries
Dependencies:abindaffyaffyioannotateAnnotationDbiAnnotationFilteraskpassassertthatbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocManagerBiocParallelBiocStylebiomaRtBiostringsbitbit64blobbookdownbslibcachemcaretcirclizeclasscliclockclueclustercodacodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDEoptimRdiagramdigestdiptestdir.expirydoParalleldplyre1071evaluatefarverfastmapfilelockflexmixFNNfontawesomeforeachformatRfpcfsfutile.loggerfutile.optionsfuturefuture.applygbmgdatagenefiltergenericsGenomicRangesggalluvialggplot2ggrepelggvisGlobalOptionsglobalsgluegowergridExtragtablegtoolshardhathexbinhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2hwriterigraphimputeipredIRangesisobanditeratorsjquerylibjsonliteKEGGRESTkernlabKernSmoothknitrlabelinglambda.rLaplacesDemonlaterlatticelavalazyevallbfgslifecyclelimmalistenvlpSolvelubridatemagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmclustmemoiseMetaboCoreUtilsmimemixtoolsmlbenchMLInterfacesModelMetricsmodeltoolsMsCoreUtilsMSnbaseMultiAssayExperimentmvtnormmzIDmzRncdf4nlmennetnumDerivopensslotelparallellypcaMethodspillarpkgconfigplotlyplsplyrpngprabcluspreprocessCoreprettyunitspROCprodlimprogressprogressrpRolocpRolocdatapromisesProtGenericsproxyPSMatchPTModspurrrQFeaturesR6randomForestrappdirsRColorBrewerRcppRcppArmadillorecipesreshape2Rhdf5librlangrmarkdownrobustbaserpartRSQLiteS4ArraysS4VectorsS7samplingsassscalessegmentedSeqinfosfsmiscshapeshinysnowsourcetoolsSparseArraysparsevctrsSpectraSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsysthreejstibbletidyrtidyselecttimechangetimeDatetinytextzdbutf8vctrsviridisviridisLitevsnwithrxfunXMLxml2xtableXVectoryaml
Vignette 1: Getting Started with BANDLE
Last update: 2024-10-23
Started: 2022-02-02
Vignette 2: A workflow for analysing differential localisation
Introduction | The data | Spatialtemporal proteomic profiling of a THP-1 cell line | Preparing the data | Preparing the bandle input parameters | Fitting Gaussian processes | Setting the prior on the weights | Running bandle | Processing and analysing the bandle results | Assessing convergence | Removing unconverged chains | Running bandleProcess and bandleSummary | Predicting subcellular location | Thresholding on the posterior probability | Distribution on allocations | Proteins assigned to one main location | Proteins with uncertainty | Differential localisation | Visualising differential localisation | Alluvial plots | Protein profiles | Session information | References
Last update: 2024-10-23
Started: 2022-02-02
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| An R package for the Bayesian analysis of differential subcellular localisation experiments | bandle-package |
| Differential localisation experiments using the bandle method | bandle diffLoc |
| Number of outliers at each iteration of MCMC | bandle_get_outliers |
| Infrastructure to to store and process MCMC results | .bandleChain .bandleChains .bandleParams .bandleSummaries .bandleSummary .nicheParam .nicheParams bandleChain-class bandleChains-class bandleJoint bandleJoint,bandleSummary-method bandleParams-class bandleSummaries-class bandleSummary-class chains length,bandleChains-method length,bandleParams-method length,bandleSummaries-method length,nicheParams-method nicheParam-class nicheParams-class params posteriorEstimates posteriorEstimates,bandleSummary-method show,bandleChain-method show,bandleChains-method show,bandleParams-method show,bandleSummaries-method show,nicheParam-method show,nicheParams-method summaries [,bandleChains,ANY,ANY,ANY-method [,bandleParams,ANY,ANY,ANY-method [,bandleSummaries,ANY,ANY,ANY-method [,nicheParams,ANY,ANY,ANY-method [[,bandleChains,ANY,ANY-method [[,bandleParams,ANY,ANY-method [[,bandleSummaries,ANY,ANY-method [[,nicheParams,ANY,ANY-method |
| Make predictions from a bandle analysis | bandlePredict |
| process bandle results | bandleProcess |
| bessel function of the second kind from boost library | besselK besselK_boost centeredData centeredDatamatern comploglike comploglikelist componentloglike dmvtCpp dmvtInt gradientamatern gradientGPcpp gradientGPcppmatern gradientrhomatern LeapfrogGPcpp LeapfrogGPcppPC likelihoodGPcpp loglikeGPcpp mahaInt makeComponent matern normalisedData normalisedDatamatern rcpp_pgdraw sampleAlloccpp sampleDirichlet sampleGPmeancpp sampleGPmeanmaterncpp sampleOutliercpp trenchDetcpp trenchInvcpp |
| Calculate the Gelman and Rubin diagnostic for bandle output | calculateGelman |
| Compute differential localisation probabilities from ms-based experiments using the bandle method | binomialDiffLocProb bootstrapdiffLocprob diffLocalisationProb |
| Compute the expected False Discovery Rate | EFDR |
| Fit a Gaussian process to spatial proteomics data | fitGP fitGPmatern fitGPmaternPC plotGPmatern |
| Container for GP results | .gpParams gpParams-class |
| Compute GP gradient | gradientGP gradientGPmatern gradientlogprior Gumbel likelihoodGP likelihoodGPmatern metropolisGP metropolisGPmatern PCrhomvar posteriorGPmatern posteriorgradientGPmatern |
| Computes the Kullback-Leibler divergence between Polya-Gamma and Dirichlet priors | kldir kldirpg prior_pred_dir prior_pred_pg |
| Generate a violin plot showing the probabilitiy of protein localisation to different organelles | mcmc_plot_probs |
| Computes Organelle means and variances using markers | meanOrganelle |
| Generates a histogram of ranks (a rank plot) for convergence | plotConvergence |
| Generate trace and density plots for all chains | plotOutliers |
| Generate a table of differential localisations | plotTable |
| Plot changes in localisation between two conditions/datasets | plotTranslocations |
| sample allocations, probabilities and compute loglikilihoods | covOrganelle outlierAllocationProbs pg_prior proteinAllocation sampleOutlier sample_weights_dir sample_weights_pg |
| robust Mahalanobis distance | mrMethod reprodScore robustMahalanobis |
| Generate a dynamic spatial proteomics experiment | sim_dynamic |
| Generate a PCA plot with smoothed probability contours | spatial2D |
| inherits StatSratum | StatStratum |