Subset an ArchRProject for downstream analysis

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

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.