getMatrixFromProject: Get a data matrix stored in an ArchRProject
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

getMatrixFromProject

R Documentation

Get a data matrix stored in an ArchRProject

Description

This function gets a given data matrix from an ArchRProject.

Usage

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.