Automatically detact the format of the input file and read the file.
readSingleCellMatrix(
file,
class = c("Matrix", "matrix"),
delayedArray = TRUE,
colIndexLocation = NULL,
rowIndexLocation = NULL
)
Path to input file. Supported file endings include .mtx, .txt,
.csv, .tab, .tsv, .npz, and their corresponding gzip
,
bzip2
, or xz
compressed extensions (*.gz
,
*.bz2
, or *.xz
).
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".
Boolean. Whether to read the expression matrix as
DelayedArray object or not. Default TRUE
.
Character. For Optimus output, the path to the
barcode index .npy file. Used only if file
has .npz extension.
Default NULL
.
Character. For Optimus output, The path to the
feature (gene) index .npy file. Used only if file
has .npz extension.
Default NULL
.
A DelayedArray object or matrix.
mat <- readSingleCellMatrix(system.file("extdata/hgmm_1k_v3_20x20/outs/",
"filtered_feature_bc_matrix/matrix.mtx.gz", package = "singleCellTK"))