Export Group Summarized Experiment — getGroupSE • ArchR

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

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.

Examples


# Get Test ArchR Project
proj <- getTestProject()

# Get Group SE
se <- getGroupSE(proj, useMatrix = "PeakMatrix", groupBy = "Clusters")