Skip to contents

Read PhysioExperiment from HDF5

Source: R/io-hdf5.R
readPhysioHDF5.Rd

Reads a PhysioExperiment object from HDF5 format. By default, returns DelayedArray-backed assays for out-of-memory processing.

Usage

readPhysioHDF5(path, as_delayed = TRUE)

Arguments

path

Path to the HDF5 file.

as_delayed

Logical. If TRUE (default), returns DelayedArray-backed assays. If FALSE, loads data into memory.

Value

A PhysioExperiment object. When as_delayed = TRUE, assays are HDF5Array objects enabling out-of-memory access; when FALSE, assays are standard in-memory arrays.

References

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

See also

writePhysioHDF5, isHDF5Backed, realizeHDF5, writeAssayHDF5

Examples

# Write a small PhysioExperiment to a temporary HDF5 file
pe <- PhysioExperiment(
  assays = list(raw = matrix(rnorm(1000), nrow = 100, ncol = 10)),
  samplingRate = 100
)
tmp <- tempfile(fileext = ".h5")
writePhysioHDF5(pe, tmp)

# Read it back with the DelayedArray backend (out-of-memory)
pe_delayed <- readPhysioHDF5(tmp)
isHDF5Backed(pe_delayed)  # TRUE
#> [1] TRUE

# Read it back into memory
pe_mem <- readPhysioHDF5(tmp, as_delayed = FALSE)
isHDF5Backed(pe_mem)  # FALSE
#> [1] FALSE

unlink(tmp)