Read a Matrix Market file

read_mtx() reads a .mtx file (Matrix Market, coordinate or array format, with the integer, real or pattern field) into an AnnData() object with a CSR X, as Python's read_mtx(). The obs and var names are "0", "1" and so on. Symmetric and skew-symmetric matrices are expanded to the full matrix.

Usage

read_mtx(filename, dtype = "float32")

Arguments

filename

A path (a .gz or .bz2 suffix is decompressed).

dtype

A numpy dtype string for X, such as "float32" (the default), "float64" or "int32". The values are R doubles that carry the On-disk dtype.

Value

An AnnData() object with a sparse (CSR) X.

Examples

path <- tempfile(fileext = ".mtx")
writeLines(
  c(
    "%%MatrixMarket matrix coordinate integer general",
    "2 3 2",
    "1 1 5",
    "2 3 7"
  ),
  path
)
read_mtx(path)
#> AnnData object with n_obs × n_vars = 2 × 3
#>     layers: None (.X)