Create ArchRProject from ArrowFiles — ArchRProject • ArchR

This function will create an ArchRProject from the provided ArrowFiles.

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)