HDF5Array (version 1.0.2)

setHDF5DumpFile: Control the location of automatically created HDF5 datasets

Description

Utility functions to control the location of automatically created HDF5 datasets.

Usage

setHDF5DumpFile(file=paste0(tempfile(), ".h5"))
getHDF5DumpFile()
lsHDF5DumpFile()
setHDF5DumpName(name)
getHDF5DumpName()

Arguments

file

The path to the current output HDF5 file, that is, to the HDF5 file where all newly created datasets shall be written.

name

The name of the next dataset to be written to the current output HDF5 file. This is for a one-time use only.

See Also

• DelayedArray objects.

• DelayedArray-utils for common operations on DelayedArray objects.

• HDF5Array objects.

• The h5ls function in the rhdf5 package, on which lsHDF5DumpFile is based.

Examples

getHDF5DumpFile()

## Use setHDF5DumpFile() to change the current output HDF5 file.
## If the specified file exists, then it must be in HDF5 format or
## an error will be raised. If it doesn't exist, then it will be
## created.
#setHDF5DumpFile("path/to/some/HDF5/file")

lsHDF5DumpFile()

a <- array(1:600, c(150, 4))
h5a <- HDF5Dataset(a)
lsHDF5DumpFile()
A <- HDF5Array(h5a)   # DelayedArray object
A

b <- array(runif(6000), c(4, 2, 150))
h5b <- HDF5Dataset(b)
lsHDF5DumpFile()
B <- HDF5Array(h5b)   # DelayedArray object
B

C <- (log(2 * A + 0.88) - 5)^3 * t(drop(B[ , 1, ]))
C
HDF5Dataset(C)        # realize C on disk
lsHDF5DumpFile()

## Matrix multiplication is not delayed:
P <- C %*% matrix(runif(20), nrow=4)
lsHDF5DumpFile()