subsetArchRProject: Subset an ArchRProject for downstream analysis
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

subsetArchRProject

R Documentation

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.