Read H5AD

Read data from a H5AD file

Usage

read_h5ad(
  path,
  as = c("InMemoryAnnData", "HDF5AnnData", "SingleCellExperiment", "Seurat"),
  to = deprecated(),
  mode = c("r", "r+", "a", "w", "w-", "x"),
  ...
)

Arguments

path

Path to the H5AD file to read

as

The type of object to return. One of:

• "InMemoryAnnData": Read the H5AD file into memory as an InMemoryAnnData object

• "HDF5AnnData": Read the H5AD file as an HDF5AnnData object

• "SingleCellExperiment": Read the H5AD file as a SingleCellExperiment::SingleCellExperiment object

• "Seurat": Read the H5AD file as a SeuratObject::Seurat object

to

Deprecated, use as instead

mode

The mode to open the HDF5 file.

• a creates a new file or opens an existing one for read/write.

• r opens an existing file for reading.

• r+ opens an existing file for read/write.

• w creates a file, truncating any existing ones.

• w-/x are synonyms, creating a file and failing if it already exists.

...

Extra arguments provided to the as_* conversion function for the object specified by as

Value

The object specified by as

See also

Other AnnData creators: AnnData(), as_AnnData()

Examples

h5ad_file <- system.file("extdata", "example.h5ad", package = "anndataR")

# Read the H5AD as a SingleCellExperiment object
if (requireNamespace("SingleCellExperiment", quietly = TRUE)) {
  sce <- read_h5ad(h5ad_file, as = "SingleCellExperiment")
}

# Read the H5AD as a Seurat object
if (requireNamespace("SeuratObject", quietly = TRUE)) {
  seurat <- read_h5ad(h5ad_file, as = "Seurat")
}