Get the fragments from an ArchRProject — getFragmentsFromProject • ArchR

This function retrieves the fragments from a given ArchRProject as a GRangesList object.

getFragmentsFromProject(
  ArchRProj = NULL,
  subsetBy = NULL,
  cellNames = NULL,
  verbose = FALSE,
  logFile = createLogFile("getFragmentsFromProject")
)

Arguments

subsetBy: A Genomic Ranges object to subset fragments by.
cellNames: A character vector indicating the cell names of a subset of cells from which fragments whould be extracted. This allows for extraction of fragments from only a subset of selected cells. By default, this function will extract all cells from the provided ArrowFile using getCellNames().
verbose: A boolean value indicating whether to use verbose output during execution of this function. Can be set to FALSE for a cleaner output.
logFile: The path to a file to be used for logging ArchR output.
ArchRProject: An ArchRProject object to get fragments from.

Examples


#Get Test Project
proj <- getTestProject()

# Get Fragments
frags <- getFragmentsFromProject(proj)