Get a data matrix stored in an ArchRProject

This function gets a given data matrix from an ArchRProject.

getMatrixFromProject(
  ArchRProj = NULL,
  useMatrix = "GeneScoreMatrix",
  useSeqnames = NULL,
  verbose = TRUE,
  binarize = FALSE,
  threads = getArchRThreads(),
  logFile = createLogFile("getMatrixFromProject")
)

Arguments

ArchRProj

An ArchRProject object to get data matrix from.

useMatrix

The name of the data matrix to retrieve from the given ArrowFile. Options include "TileMatrix", "GeneScoreMatrix", etc.

useSeqnames

A character vector of chromosome names to be used to subset the data matrix being obtained.

verbose

A boolean value indicating whether to use verbose output during execution of this function. Can be set to FALSE for a cleaner output.

binarize

A boolean value indicating whether the matrix should be binarized before return. This is often desired when working with insertion counts.

logFile

The path to a file to be used for logging ArchR output.