subsetArchRProject: Subset an ArchRProject for downstream analysis

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

Subset an ArchRProject for downstream analysis

Description

This function will subset and ArchRProject by cells and save the output to a new directory and re-load the subsetted ArchRProject.

Usage

subsetArchRProject(
  ArchRProj = NULL,
  cells = getCellNames(ArchRProj),
  outputDirectory = "ArchRSubset",
  dropCells = TRUE,
  logFile = NULL,
  threads = getArchRThreads(),
  force = FALSE
)

Arguments

ArchRProj	An ArchRProject object.
cells	A vector of cells to subset ArchRProject by. Alternatively can provide a subset ArchRProject.
outputDirectory	A directory path to save all ArchR output and the subsetted ArchRProject to.
dropCells	A boolean indicating whether to drop cells that are not in ArchRProject from corresponding Arrow Files.
logFile	The path to a file to be used for logging ArchR output.
threads	The number of threads to use for parallel execution.
force	If output directory exists overwrite.

Examples

# Get Small Test Project
proj <- getTestProject()

#Subset
proj <- subsetArchRProject(proj, cells = getCellNames(proj)[1:50])

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