Get a data matrix stored in an ArrowFile — getMatrixFromArrow • ArchR

This function gets a given data matrix from an individual ArrowFile.

getMatrixFromArrow(
  ArrowFile = NULL,
  useMatrix = "GeneScoreMatrix",
  useSeqnames = NULL,
  excludeChr = NULL,
  cellNames = NULL,
  ArchRProj = NULL,
  verbose = TRUE,
  binarize = FALSE,
  logFile = createLogFile("getMatrixFromArrow")
)

Arguments

ArrowFile: The path to an ArrowFile from which the selected data matrix should be obtained.
useMatrix: The name of the data matrix to retrieve from the given ArrowFile. Options include "TileMatrix", "GeneScoreMatrix", etc.
useSeqnames: A character vector of chromosome names to be used to subset the data matrix being obtained.
excludeChr: A character vector containing the seqnames of the chromosomes that should be excluded from this analysis.
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().
ArchRProj: An ArchRProject object to be used for getting additional information for cells in cellColData. In some cases, data exists within the ArchRProject object that does not exist within the ArrowFiles. To access this data, you can provide the ArchRProject object here.
verbose: A boolean value indicating whether to use verbose output during execution of this function. Can be set to FALSE for a cleaner output.
binarize: A boolean value indicating whether the matrix should be binarized before return. This is often desired when working with insertion counts.
logFile: The path to a file to be used for logging ArchR output.

Examples


#Get Test Arrow
arrow <- getTestArrow()

# Get Fragments
se <- getMatrixFromArrow(arrow)