bioconductor-bandle

name	bioconductor-bandle
description	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.

bandle

Workflows

Standard Workflow

Perform differential subcellular localisation analysis on mass-spectrometry-based spatial proteomics data across two conditions.

library(bandle)
library(pRolocdata)
data("tan2009r1")

# 1. Load User Input and Extract Common Features (simulated here)
tansim <- sim_dynamic(object = tan2009r1, numRep = 6L, numDyn = 100L)
control <- tansim$lopitrep[1:3]
treatment <- tansim$lopitrep[4:6]

# 2. Fit Gaussian Processes to Marker Profiles
gpParams <- lapply(tansim$lopitrep, function(x) fitGPmaternPC(x))

# 3. Set Up and Check Dirichlet Prior
K <- length(getMarkerClasses(tansim$lopitrep[[1]], fcol = "markers"))
dirPrior <- diag(rep(1, K)) + matrix(0.001, nrow = K, ncol = K)
predDirPrior <- prior_pred_dir(object = tansim$lopitrep[[1]], dirPrior = dirPrior, q = 15)

# 4. Run BANDLE MCMC
pc_prior <- matrix(rep(c(10, 60, 250), each = K), ncol = 3)
bandleres <- bandle(objectCond1 = control, objectCond2 = treatment, 
                    numIter = 100, burnin = 5L, thin = 1L, 
                    gpParams = gpParams, pcPrior = pc_prior, 
                    numChains = 3, dirPrior = dirPrior, seed = 1)

# 5. Assess MCMC Convergence
calculateGelman(bandleres)
plotOutliers(bandleres)

# 6. Extract Differential Localisation Probabilities
bandleres_opt <- bandleProcess(bandleres)
xx <- bandlePredict(control, treatment, params = bandleres_opt, fcol = "markers")
res_control <- xx[[1]]
res_treatment <- xx[[2]]

Input: Replicated MSnSet objects for control and treatment conditions. Output: A list of MSnSet objects with appended subcellular allocation probabilities and differential localisation predictions.

When to Use

• Analyzing differential subcellular localisation of proteins across two conditions (e.g., control vs. treatment) using mass-spectrometry-based spatial proteomics data.
• Quantifying uncertainty in protein subcellular assignments using Bayesian posterior distributions.
• Fitting non-parametric regression functions to marker profiles using Gaussian processes with fitGPmaternPC().

When NOT to Use

• For standard differential expression/abundance analysis of proteins; use MSstats instead.
• For simple static subcellular localisation without a comparative/differential design; use pRoloc instead.

Data Requirements

• Input data must be stored as MSnSet instances (from MSnbase).
• Requires replicate experiments for both conditions (e.g., control and treatment).
• Requires predefined marker proteins annotated in the feature data (e.g., fcol = "markers").

Key Parameters

• objectCond1: List of MSnSet objects for condition 1 (control).
• objectCond2: List of MSnSet objects for condition 2 (treatment).
• numIter: Number of MCMC iterations (typically 10,000).
• burnin: Number of burn-in iterations to discard (typically 5,000).
• thin: Thinning interval for MCMC sampling (typically 20).
• gpParams: Gaussian Process parameters obtained from fitGPmaternPC().
• pcPrior: Penalised complexity prior matrix for the Gaussian Processes.
• dirPrior: Dirichlet prior matrix on the mixing weights.

Best Practices

• Visually evaluate the fit of the Gaussian Processes to marker profiles using plotGPmatern() before running the main MCMC.
• Run at least 4 parallel chains and a high number of iterations (e.g., 10,000) to ensure robust posterior sampling.
• Assess MCMC convergence using calculateGelman() (ratios should be < 1.2) and plotOutliers() before interpreting results.
• Remove unconverged chains using standard subsetting (e.g., bandleres[-2]) before running bandleProcess().

Common Pitfalls

• Running too few MCMC iterations: Leads to poor convergence and unreliable probability estimates. Fix: Increase numIter to 10,000 and burnin to 5,000.
• Including unconverged chains in downstream analysis: Distorts posterior probability distributions. Fix: Subset the bandleParams object to exclude bad chains before processing.

Alternatives

• pRoloc: For static (single-condition) spatial proteomics and organelle assignment.
• MSnbase: For basic mass spectrometry data structures and processing.

Citations

• Crook et al. 2022, bioRxiv/journal (for BANDLE).
• Crook et al. 2018, PLOS Computational Biology (for TAGM).

References

• Homepage: bioconductor.org/packages/bandle
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/bandle/inst/doc/vignette1-getting-started.html