Get the fragments from an ArrowFile — getFragmentsFromArrow • ArchR

This function retrieves the fragments from a given ArrowFile as a GRanges object.

getFragmentsFromArrow(
  ArrowFile = NULL,
  chr = NULL,
  cellNames = NULL,
  verbose = TRUE,
  logFile = createLogFile("getFragmentsFromArrow")
)

Arguments

ArrowFile: The path to the ArrowFile from which fragments should be obtained.
chr: A name of a chromosome to be used to subset the fragments GRanges object to a specific chromsome if desired.
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.


#Get Test Arrow
arrow <- getTestArrow()

# Get Fragments
frags <- getFragmentsFromArrow(arrow)