h5ReadDataset {hdf5r.Extra}

Read data from an existing H5 dataset

Description

Low-level helper function to read atomic R data from an existing H5 dataset.

Usage

h5ReadDataset(x, ...)

## S3 method for class 'H5D'
h5ReadDataset(x, idx_list = NULL, transpose = FALSE, ...)

## S3 method for class 'H5Group'
h5ReadDataset(x, name, idx_list = NULL, transpose = FALSE, ...)

## S3 method for class 'H5File'
h5ReadDataset(x, name, idx_list = NULL, transpose = FALSE, ...)

## S3 method for class 'character'
h5ReadDataset(x, name, transpose = FALSE, idx_list = NULL, ...)

Arguments

x

An H5File, H5Group, H5D or a path name of HDF5 file.

...

Arguments passed to H5D$read().

idx_list

The indices for each dimension of name to subset given as a list. If NULL, the entire dataset will be read. Passed to H5D$read(args).

transpose

Whether or not to transpose the read matrix. Only works for a 2-dimension array-like data.

name

Name of the HDF5 link to be read. Must be an H5 dataset.

Value

An array-like object with the data read.

Examples

file <- system.file("extdata", "pbmc_small.h5ad", package = "hdf5r.Extra")

x <- h5ReadDataset(file, name = "X")
x <- h5ReadDataset(file, name = "X", transpose = TRUE)
x <- h5ReadDataset(file, name = "X", idx_list = list(1:10, 1:20))
x <- h5ReadDataset(
  file, 
  name = "X", 
  idx_list = list(1:10, 1:20), 
  transpose = TRUE
)