getGroupSE: Export Group Summarized Experiment
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

getGroupSE

R Documentation

Export Group Summarized Experiment

Description

This function will group, summarize and export a summarized experiment for a assay in a ArchRProject.

Usage

getGroupSE(
  ArchRProj = NULL,
  useMatrix = NULL,
  groupBy = "Sample",
  divideN = TRUE,
  scaleTo = NULL,
  threads = getArchRThreads(),
  verbose = TRUE,
  logFile = createLogFile("getGroupSE")
)

Arguments

`ArchRProj`	An `ArchRProject` object.
`useMatrix`	The name of the matrix in the ArrowFiles. See getAvailableMatrices to see options
`groupBy`	The name of the column in `cellColData` to use for grouping cells together for summarizing.
`divideN`	A boolean describing whether to divide by the number of cells.
`scaleTo`	Depth normalize to this value if not NULL.
`threads`	An integer specifying the number of threads for parallel.
`verbose`	A boolean specifying to print messages during computation.
`logFile`	The path to a file to be used for logging ArchR output.