celdaGridSearch {celda} | R Documentation

## Run Celda in parallel with multiple parameters

### Description

Run Celda with different combinations of parameters and multiple chains in parallel. The variable 'availableModels' contains the potential models that can be utilized. Different parameters to be tested should be stored in a list and passed to the argument 'paramsTest'. Fixed parameters to be used in all models, such as 'sampleLabel', can be passed as a list to the argument 'paramsFixed'. When 'verbose = TRUE', output from each chain will be sent to a log file but not be displayed in stdout.

### Usage

    celdaGridSearch(
      counts,
      model,
      paramsTest,
      paramsFixed = NULL,
      maxIter = 200,
      nchains = 3,
      cores = 1,
      bestOnly = TRUE,
      perplexity = TRUE,
      verbose = TRUE,
      logfilePrefix = "Celda"
    )

### Arguments

`counts` | Integer matrix. Rows represent features and columns represent cells.
`model` | Celda model. Options available in 'celda::availableModels'.
`paramsTest` | List. A list denoting the combinations of parameters to run in a celda model. For example, 'list(K = seq(5, 10), L = seq(15, 20))' will run all combinations of K from 5 to 10 and L from 15 to 20 in model 'celda_CG()'.
`paramsFixed` | List. A list denoting additional parameters to use in each celda model. Default NULL.
`maxIter` | Integer. Maximum number of iterations of sampling to perform. Default 200.
`nchains` | Integer. Number of random cluster initializations. Default 3.
`cores` | Integer. The number of cores to use for parallel estimation of chains. Default 1.
`bestOnly` | Logical. Whether to return only the chain with the highest log likelihood per combination of parameters or return all chains. Default TRUE.
`perplexity` | Logical. Whether to calculate perplexity for each model. If FALSE, then perplexity can be calculated later with 'resamplePerplexity()'. Default TRUE.
`verbose` | Logical. Whether to print log messages during celda chain execution. Default TRUE.
`logfilePrefix` | Character. Prefix for log files from worker threads and main process. Default "Celda".

### Value

Object of class 'celdaList', which contains results for all model parameter combinations and summaries of the run parameters

### See Also

'celda_G()' for feature clustering, 'celda_C()' for clustering of cells, and 'celda_CG()' for simultaneous clustering of features and cells. 'subsetCeldaList()' can subset the 'celdaList' object. 'selectBestModel()' can get the best model for each combination of parameters.

### Examples

    data(celdaCGSim)
    #' ## Run various combinations of parameters with 'celdaGridSearch'
    celdaCGGridSearchRes <- celdaGridSearch(celdaCGSim$counts,
        model = "celda_CG",
        paramsTest = list(K = seq(4, 6), L = seq(9, 11)),
        paramsFixed = list(sampleLabel = celdaCGSim$sampleLabel),
        bestOnly = TRUE,
        nchains = 1,
        cores = 2)

[Package celda version 1.3.4 Index]