ArchRProject: Create ArchRProject from ArrowFiles

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

Create ArchRProject from ArrowFiles

Description

This function will create an ArchRProject from the provided ArrowFiles.

Usage

ArchRProject(
  ArrowFiles = NULL,
  outputDirectory = "ArchROutput",
  copyArrows = TRUE,
  geneAnnotation = getGeneAnnotation(),
  genomeAnnotation = getGenomeAnnotation(),
  showLogo = TRUE,
  threads = getArchRThreads()
)

Arguments

ArrowFiles	A character vector containing the relative paths to the ArrowFiles to be used.
outputDirectory	A name for the relative path of the outputDirectory for ArchR results. Relative to the current working directory.
copyArrows	A boolean value indicating whether ArrowFiles should be copied into outputDirectory.
geneAnnotation	The geneAnnotation object (see createGeneAnnotation()) to be used for downstream analyses such as calculating TSS Enrichment Scores, Gene Scores, etc.
genomeAnnotation	The genomeAnnotation object (see createGenomeAnnotation()) to be used for downstream analyses requiring genome information such as nucleotide information or chromosome sizes.
showLogo	A boolean value indicating whether to show the ascii ArchR logo after successful creation of an ArchRProject.
threads	The number of threads to use for parallel execution.

Examples

# Get Test Arrow
arrow <- getTestArrow()

# Create ArchR Project for Analysis
proj <- ArchRProject(arrow)   

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