Read single cell expression matrix — readSingleCellMatrix • singleCellTK

Automatically detact the format of the input file and read the file.

readSingleCellMatrix(
  file,
  class = c("Matrix", "matrix"),
  delayedArray = TRUE,
  colIndexLocation = NULL,
  rowIndexLocation = NULL
)

Arguments

file: 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).
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 TRUE.
colIndexLocation: Character. For Optimus output, the path to the barcode index .npy file. Used only if file has .npz extension. Default NULL.
rowIndexLocation: 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"))