Automatically detact the format of the input file and read the file.
readSingleCellMatrix( file, class = c("Matrix", "matrix"), delayedArray = TRUE, colIndexLocation = NULL, rowIndexLocation = NULL )
file | Path to input file. Supported file endings include .mtx, .txt,
.csv, .tab, .tsv, .npz, and their corresponding |
---|---|
class | Character. Class of matrix. One of "Matrix" or "matrix". Specifying "Matrix" will convert to a sparse format which should be used for datasets with large numbers of cells. Default "Matrix". |
delayedArray | Boolean. Whether to read the expression matrix as
DelayedArray object or not. Default |
colIndexLocation | Character. For Optimus output, the path to the
barcode index .npy file. Used only if |
rowIndexLocation | Character. For Optimus output, The path to the
feature (gene) index .npy file. Used only if |
A DelayedArray object or matrix.
mat <- readSingleCellMatrix(system.file("extdata/hgmm_1k_v3_20x20/outs/", "filtered_feature_bc_matrix/matrix.mtx.gz", package = "singleCellTK"))