getGroupSE: Export Group Summarized Experiment

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

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.

Examples

# Get Test ArchR Project
proj <- getTestProject()

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

GreenleafLab/ArchR documentation built on Feb. 21, 2025, 3:05 p.m.