Read an HDF5 file with a data matrix — read

read_hdf() reads the dataset key of an HDF5 (.h5) file into the X of an AnnData() object, as Python's read_hdf(). If the file also has the datasets row_names and col_names they become the obs and var names.

Usage

read_hdf(filename, key)

Arguments

filename: A path to the HDF5 file.
key: The name of the dataset holding the matrix. An empty string is an error that lists the datasets in the file.

Value

An AnnData() object.

Examples

path <- tempfile(fileext = ".h5")
rhdf5::h5createFile(path)
rhdf5::h5write(matrix(c(0.5, 1.5, 2.5, 3.5), 2), path, "data")
read_hdf(path, "data")
#> AnnData object with n_obs × n_vars = 2 × 2
#>     layers: None (.X)