getMatrixFromArrow.Rd
This function gets a given data matrix from an individual ArrowFile.
getMatrixFromArrow( ArrowFile = NULL, useMatrix = "GeneScoreMatrix", useSeqnames = NULL, cellNames = NULL, ArchRProj = NULL, verbose = TRUE, binarize = FALSE, logFile = createLogFile("getMatrixFromArrow") )
ArrowFile | The path to an ArrowFile from which the selected data matrix should be obtained. |
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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. |
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 |
ArchRProj | An |
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. |