HDF5ArraySeed-class {HDF5Array} | R Documentation

## HDF5ArraySeed objects

### Description

HDF5ArraySeed is a low-level helper class for representing a pointer to an HDF5 dataset.

Note that an HDF5ArraySeed object is not intended to be used directly. Most end users will typically create and manipulate a higher-level HDF5Array object instead. See `?HDF5Array` for more information.

### Usage

    ## --- Constructor function ---

    HDF5ArraySeed(filepath, name, as.sparse=FALSE, type=NA)

    ## --- Accessors --------------

    ## S4 method for signature 'HDF5ArraySeed'
    path(object)

    ## S4 replacement method for signature 'HDF5ArraySeed'
    path(object) <- value

    ## S4 method for signature 'HDF5ArraySeed'
    dim(x)

    ## S4 method for signature 'HDF5ArraySeed'
    dimnames(x)

    ## S4 method for signature 'HDF5ArraySeed'
    type(x)

    ## S4 method for signature 'HDF5ArraySeed'
    is_sparse(x)

    ## S4 replacement method for signature 'HDF5ArraySeed'
    is_sparse(x) <- value

    ## S4 method for signature 'HDF5ArraySeed'
    chunkdim(x)

    ## --- Data extraction --------

    ## S4 method for signature 'HDF5ArraySeed'
    extract_array(x, index)

    ## S4 method for signature 'HDF5ArraySeed'
    extract_sparse_array(x, index)

### Arguments

`filepath, name, as.sparse, type` | See `?HDF5Array` for a description of these arguments.
`object, x` | An HDF5ArraySeed object or derivative.
`value` | For the `path()` setter: The new path (as a single string) to the HDF5 file where the dataset is located. For the `is_sparse()` setter: `TRUE` or `FALSE`.
`index` | See `?extract_array` in the DelayedArray package.

### Details

The HDF5ArraySeed class has one direct subclass: Dense_H5ADMatrixSeed. See `?Dense_H5ADMatrixSeed` for more information.

Note that the implementation of HDF5ArraySeed objects follows the widely adopted convention of transposing HDF5 matrices when they get loaded into R.

Finally note that an HDF5ArraySeed object supports a very limited set of methods:

- `path()`: Returns the path to the HDF5 file where the dataset is located.

- `dim()`, `dimnames()`.

- `type()`, `is_sparse()`, `chunkdim()`, `extract_array()`, `extract_sparse_array()`: These generics are defined and documented in the DelayedArrray package.

### Value

`HDF5ArraySeed()` returns an HDF5ArraySeed object.

### HDF5ArraySeed vs HDF5Array objects

In order to have access to the full set of operations that are available for DelayedArray objects, an HDF5ArraySeed object first needs to be wrapped in a DelayedArray object, typically by calling the `DelayedArray()` constructor on it.

This is what the `HDF5Array()` constructor function does.

Note that the result of this wrapping is an HDF5Array object, which is just an HDF5ArraySeed object wrapped in a DelayedArray object.

### See Also

- HDF5Array objects.

- `h5ls` to list the content of an HDF5 file.

### Examples

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

    DelayedArray(seed1)
    stopifnot(class(DelayedArray(seed1)) == "HDF5Array")

[Package HDF5Array version 1.20.0 Index]