h5Open: Open an HDF5 file, file-handler or group object

In hdf5r.Extra: Extensions for 'HDF5' R Interfaces

Open an HDF5 file, file-handler or group object

Description

Open an HDF5 file, file-handler or group object

Usage

h5Open(x, name, ...)

## S3 method for class 'H5Group'
h5Open(x, name, ...)

## S3 method for class 'H5File'
h5Open(x, name, ...)

## S3 method for class 'character'
h5Open(x, name, mode = c("a", "r", "r+", "w", "w-", "x"), ...)

Arguments

x	An H5File, H5Group or a path name of HDF5 file.
name	Name of the opened HDF5 link.
...	Arguments passed to H5Group$open(). #' @details For an H5File or a HDF5 file, 'name' will be treated as absolute path using h5AbsLinkName.
mode	Passed to h5TryOpen

Value

An opened H5File, H5Group or H5D.

• When x is an H5File or a file path, name = "/" should always return an H5File.

• When x is an H5Group, name = "/" should raise an error.

Examples

file <- system.file("extdata", "pbmc_small.h5ad", package = "hdf5r.Extra")
obs <- h5Open(file, "obs", mode = "r")
inherits(obs, "H5Group")

h5fh <- h5Open(file, "/", mode = "r")
inherits(h5fh, "H5File")

tsne <- h5Open(file, "obsm/tsne", mode = "r")
inherits(tsne, "H5D")

try(h5Open(obs, "/"))  ## Error

hdf5r.Extra documentation built on Oct. 18, 2024, 9:06 a.m.