CoGAPS {CoGAPS} | R Documentation

## CoGAPS Matrix Factorization Algorithm

### Description

calls the C++ MCMC code and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix

### Usage

    CoGAPS(
      data,
      params = new("CogapsParams"),
      nThreads = 1,
      messages = TRUE,
      outputFrequency = 1000,
      uncertainty = NULL,
      checkpointOutFile = "gaps_checkpoint.out",
      checkpointInterval = 0,
      checkpointInFile = NULL,
      transposeData = FALSE,
      BPPARAM = NULL,
      workerID = 1,
      asynchronousUpdates = TRUE,
      nSnapshots = 0,
      snapshotPhase = "sampling",
      ...
    )

### Arguments

`data` | File name or R object (see details for supported types)
`params` | CogapsParams object
`nThreads` | maximum number of threads to run on
`messages` | T/F for displaying output
`outputFrequency` | number of iterations between each output (set to 0 to disable status updates, other output is controlled by @code messages)
`uncertainty` | uncertainty matrix - either a matrix or a supported file type
`checkpointOutFile` | name of the checkpoint file to create
`checkpointInterval` | number of iterations between each checkpoint (set to 0 to disable checkpoints)
`checkpointInFile` | if this is provided, CoGAPS runs from the checkpoint contained in this file
`transposeData` | T/F for transposing data while reading it in - useful for data that is stored as samples x genes since CoGAPS requires data to be genes x samples
`BPPARAM` | BiocParallel backend
`workerID` | if calling CoGAPS in parallel the worker ID can be specified, only worker 1 prints output and each worker outputs when it finishes, this is not neccesary when using the default parallel methods (i.e. distributed CoGAPS) but only when the user is manually calling CoGAPS in parallel
`asynchronousUpdates` | enable asynchronous updating which allows for multi-threaded runs
`nSnapshots` | how many snapshots to take in each phase, setting this to 0 disables snapshots
`snapshotPhase` | which phase to take snapsjots in e.g. "equilibration", "sampling", "all"
`...` | allows for overwriting parameters in params

### Details

The supported R types are: matrix, data.frame, SummarizedExperiment, SingleCellExperiment. The supported file types are csv, tsv, and mtx.

### Value

CogapsResult object

### Examples

    # Running from R object
    data(GIST)
    resultA <- CoGAPS(GIST.data_frame, nIterations=25)

    # Running from file name
    gist_path <- system.file("extdata/GIST.mtx", package="CoGAPS")
    resultB <- CoGAPS(gist_path, nIterations=25)

    # Setting Parameters
    params <- new("CogapsParams")
    params <- setParam(params, "nPatterns", 3)
    resultC <- CoGAPS(GIST.data_frame, params, nIterations=25)

[Package CoGAPS version 3.14.0 Index]