Virtually reshaped HDF5 datasets as DelayedArray objects
The ReshapedHDF5Array class is a DelayedArray subclass for representing an HDF5 dataset with a user-supplied upfront virtual reshaping.
All the operations available for DelayedArray objects work on ReshapedHDF5Array objects.
## Constructor function: ReshapedHDF5Array(filepath, name, dim, type=NA)
filepath, name, type |
See |
dim |
A vector of dimensions that describes the virtual reshaping i.e. the reshaping that is virtually applied upfront to the HDF5 dataset when the ReshapedHDF5Array object gets constructed. Note that the HDF5 dataset is treated as read-only so is not effectively reshaped, that is, the dataset dimensions encoded in the HDF5 file are not mmodified. Also please note that arbitrary reshapings are not supported. Only reshapings that reduce the number of dimensions by collapsing a group of consecutive dimensions into a single dimension are supported. For example, reshaping a 10 x 3 x 5 x 1000 array as a 10 x 15 x 1000 array or as a 150 x 1000 matrix is supported. |
A ReshapedHDF5Array object.
HDF5Array objects for representing HDF5 datasets as DelayedArray objects without upfront virtual reshaping.
DelayedArray objects in the DelayedArray package.
writeHDF5Array for writing an array-like object
to an HDF5 file.
saveHDF5SummarizedExperiment and
loadHDF5SummarizedExperiment in this
package (the HDF5Array package) for saving/loading
an HDF5-based SummarizedExperiment
object to/from disk.
The ReshapedHDF5ArraySeed helper class.
h5ls in the rhdf5 package.
library(h5vcData)
tally_file <- system.file("extdata", "example.tally.hfs5",
package="h5vcData")
library(rhdf5) # for h5ls()
h5ls(tally_file)
## Pick up "Coverages" dataset for Human chromosome 16 and collapse its
## first 2 dimensions:
cvg <- ReshapedHDF5Array(tally_file, "/ExampleStudy/16/Coverages",
dim=c(12, 90354753))
cvg
is(cvg, "DelayedArray") # TRUE
seed(cvg)
path(cvg)
dim(cvg)
chunkdim(cvg)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.