tagmMcmcTrain {pRoloc} | R Documentation

## Localisation of proteins using the TAGM MCMC method

### Description

These functions implement the T augmented Gaussian mixture (TAGM) model for mass spectrometry-based spatial proteomics datasets using Markov-chain Monte-Carlo (MCMC) for inference.

### Usage

    tagmMcmcTrain(object, fcol = "markers", method = "MCMC",
      numIter = 1000L, burnin = 100L, thin = 5L, mu0 = NULL,
      lambda0 = 0.01, nu0 = NULL, S0 = NULL, beta0 = NULL, u = 2,
      v = 10, numChains = 4L, BPPARAM = BiocParallel::bpparam())

    tagmMcmcPredict(object, params, fcol = "markers", probJoint = FALSE,
      probOutlier = TRUE)

    tagmPredict(object, params, fcol = "markers", probJoint = FALSE,
      probOutlier = TRUE)

    tagmMcmcProcess(params)

### Arguments

`object` | An `MSnbase::MSnSet` containing the spatial proteomics data to be passed to `tagmMcmcTrain` and `tagmPredict`.
`fcol` | The feature meta-data containing marker definitions. Default is `markers`.
`method` | A `charachter()` describing the inference method for the TAGM algorithm. Default is `"MCMC"`.
`numIter` | The number of iterations of the MCMC algorithm. Default is 1000.
`burnin` | The number of samples to be discarded from the begining of the chain. Default is 100.
`thin` | The thinning frequency to be applied to the MCMC chain. Default is 5.
`mu0` | The prior mean. Default is `colMeans` of the expression data.
`lambda0` | The prior shrinkage. Default is 0.01.
`nu0` | The prior degreed of freedom. Default is `ncol(exprs(object)) + 2`
`S0` | The prior inverse-wishart scale matrix. Empirical prior used by default.
`beta0` | The prior Dirichlet distribution concentration. Default is 1 for each class.
`u` | The prior shape parameter for Beta(u, v). Default is 2
`v` | The prior shape parameter for Beta(u, v). Default is 10.
`numChains` | The number of parrallel chains to be run. Default it 4.
`BPPARAM` | Support for parallel processing using the `BiocParallel` infrastructure. When missing (default), the default registered `BiocParallelParam` parameters are used. Alternatively, one can pass a valid `BiocParallelParam` parameter instance: `SnowParam`, `MulticoreParam`, `DoparParam`, ... see the `BiocParallel` package for details.
`params` | An instance of class `MCMCParams`, as generated by `tagmMcmcTrain()`.
`probJoint` | A `logical(1)` indicating whether to return the joint probability matrix, i.e. the probability for all classes as a new `tagm.mcmc.joint` feature variable.
`probOutlier` | A `logical(1)` indicating whether to return the probability of being an outlier as a new `tagm.mcmc.outlier` feature variable. A high value indicates that the protein is unlikely to belong to any annotated class (and is hence considered an outlier).

### Details

The `tagmMcmcTrain` function generates the samples from the posterior distributions (object or class `MCMCParams`) based on an annotated quantitative spatial proteomics dataset (object of class `MSnbase::MSnSet`). Both are then passed to the `tagmPredict` function to predict the sub-cellular localisation of protein of unknown localisation. See the pRoloc-bayesian vignette for details and examples. In this implementation, if numerical instability is detected in the covariance matrix of the data a small multiple of the identity is added. A message is printed if this conditioning step is performed.

### Value

`tagmMcmcTrain` returns an instance of class `MCMCParams`.

`tagmMcmcPredict` returns an instance of class `MSnbase::MSnSet` containing the localisation predictions as a new `tagm.mcmc.allocation` feature variable. The allocation probability is encoded as `tagm.mcmc.probability` (corresponding to the mean of the distribution probability). In additionm the upper and lower quantiles of the allocation probability distribution are available as `tagm.mcmc.probability.lowerquantile` and `tagm.mcmc.probability.upperquantile` feature variables. The Shannon entropy is available in the `tagm.mcmc.mean.shannon` feature variable, measuring the uncertainty in the allocations (a high value representing high uncertainty; the highest value is the natural logarithm of the number of classes).

`tagmMcmcProcess` returns an instance of class `MCMCParams` with its summary slot populated.

### References

A Bayesian Mixture Modelling Approach For Spatial Proteomics Oliver M Crook, Claire M Mulvey, Paul D. W. Kirk, Kathryn S Lilley, Laurent Gatto bioRxiv 282269; doi: https://doi.org/10.1101/282269

### See Also

The `plotEllipse()` function can be used to visualise TAGM models on PCA plots with ellipses.

[Package pRoloc version 1.24.1 Index]