CoGAPS: CoGAPS Matrix Factorization Algorithm

In CoGAPS: Coordinated Gene Activity in Pattern Sets

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)

CoGAPS documentation built on Nov. 8, 2020, 5:02 p.m.