HDF5 Backend for PhysioExperiment

Functions for reading and writing PhysioExperiment objects to HDF5 format, supporting out-of-memory operations for large datasets. Write PhysioExperiment to HDF5

Usage

writePhysioHDF5(
  x,
  path,
  overwrite = FALSE,
  chunk_dims = NULL,
  compression_level = 6L
)

Arguments

x: A PhysioExperiment object.
path: Path to the output HDF5 file.
overwrite: Logical. If TRUE, overwrites existing file.
chunk_dims: Optional integer vector specifying chunk dimensions for HDF5 storage. If NULL, defaults are chosen automatically.
compression_level: Integer compression level (0-9). Default is 6.

Value

Invisible NULL. The HDF5 file is written to path as a side effect.

Details

Saves a PhysioExperiment object to HDF5 format, enabling out-of-memory access for large datasets.

References

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

Examples

# Create a PhysioExperiment
pe <- PhysioExperiment(
  assays = list(raw = matrix(rnorm(1000), nrow = 100, ncol = 10)),
  samplingRate = 100
)

# Save to a temporary HDF5 file with compression
tmp <- tempfile(fileext = ".h5")
writePhysioHDF5(pe, tmp, compression_level = 6)

# Overwrite the existing file
writePhysioHDF5(pe, tmp, overwrite = TRUE)

unlink(tmp)