HDF5Array: HDF5ArraySeed-class – R documentation

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HDF5ArraySeed-class

HDF5ArraySeed objects

Description

HDF5ArraySeed is a low-level helper class for representing a pointer to an HDF5 dataset. HDF5ArraySeed objects are not intended to be used directly. Most end users should create and manipulate HDF5Array objects instead. See ?HDF5Array for more information.

Usage

## Constructor function:
HDF5ArraySeed(filepath, name, as.sparse=FALSE, type=NA)

Arguments

filepath, name, as.sparse, type

See ?HDF5Array for a description of these arguments.

Details

No operation can be performed directly on an HDF5ArraySeed object. It first needs to be wrapped in a DelayedArray object. The result of this wrapping is an HDF5Array object (an HDF5Array object is just an HDF5ArraySeed object wrapped in a DelayedArray object).

Value

An HDF5ArraySeed object.

Examples

library(h5vcData)
tally_file <- system.file("extdata", "example.tally.hfs5",
                          package="h5vcData")

library(rhdf5)  # for h5ls()
h5ls(tally_file)

name <- "/ExampleStudy/16/Coverages"  # name of the dataset of interest
seed1 <- HDF5ArraySeed(tally_file, name)
seed1
path(seed1)
dim(seed1)
chunkdim(seed1)

seed2 <- HDF5ArraySeed(tally_file, name, as.sparse=TRUE)
seed2

## Alternatively:
is_sparse(seed1) <- TRUE
seed1  # same as 'seed2'

HDF5Array

HDF5 backend for DelayedArray objects

v1.18.1

Artistic-2.0

Authors

Hervé Pagès

Initial release