Realize HDF5-backed data to memory — realizeHDF5 • PhysioIO

Loads HDF5-backed assays into memory as regular arrays.

Usage

realizeHDF5(x, assays = NULL)

Arguments

x: A PhysioExperiment object.
assays: Optional character vector of assay names to realize. If NULL, realizes all assays.

Value

A PhysioExperiment object with the specified assays realized as in-memory arrays.

References

The HDF Group (1997-2024). "Hierarchical Data Format, version 5." https://www.hdfgroup.org/HDF5/

See also

readPhysioHDF5, writePhysioHDF5, isHDF5Backed

Examples

# Write and read back HDF5-backed data
pe <- PhysioExperiment(
  assays = list(raw = matrix(rnorm(1000), nrow = 100, ncol = 10)),
  samplingRate = 100
)
tmp <- tempfile(fileext = ".h5")
writePhysioHDF5(pe, tmp)
pe_delayed <- readPhysioHDF5(tmp)

# Realize all assays to memory
pe_mem <- realizeHDF5(pe_delayed)
isHDF5Backed(pe_mem)  # FALSE
#> [1] FALSE

unlink(tmp)