saveHDF5SummarizedExperiment {HDF5Array} | R Documentation

## Save/load an HDF5-based SummarizedExperiment object

### Description

`saveHDF5SummarizedExperiment` and `loadHDF5SummarizedExperiment` can be used to save/load an HDF5-based SummarizedExperiment object to/from disk.

### Usage

    saveHDF5SummarizedExperiment(x, dir="my_h5_se", replace=FALSE,
                                 chunkdim=NULL, level=NULL, verbose=FALSE)
    loadHDF5SummarizedExperiment(dir="my_h5_se")

### Arguments

`x` | A SummarizedExperiment object.
`dir` | The path (as a single string) to the directory where to save the HDF5-based SummarizedExperiment object or to load it from. When saving, the directory will be created so should not already exist, unless `replace` is set to `TRUE`.
`replace` | If directory `dir` already exists, should it be replaced with a new one? The content of the existing directory will be lost!
`chunkdim, level` | The dimensions of the chunks and the compression level to use for writing the assay data to disk. Passed to the internal calls to `writeHDF5Array`. See `?writeHDF5Array` for more information.
`verbose` | Set to `TRUE` to make the function display progress.

### Details

These functions use functionalities from the SummarizedExperiment package internally and so require this package to be installed.

`saveHDF5SummarizedExperiment` creates the directory specified thru the `dir` argument and then populates it with the HDF5 datasets (one per assay in `x`) plus a serialized version of `x` that contains pointers to these datasets. This directory provides a self-contained HDF5-based representation of `x` that can then be loaded back in R with `loadHDF5SummarizedExperiment`. Note that this directory is relocatable i.e. it can be moved (or copied) to a different place, on the same or a different computer, before calling `loadHDF5SummarizedExperiment` on it. For convenient sharing with collaborators, it is suggested to turn it into a tarball (with Unix command `tar`), or zip file, before the transfer. Please keep in mind that `saveHDF5SummarizedExperiment` and `loadHDF5SummarizedExperiment` don't know how to produce/read tarballs or zip files at the moment, so the process of packaging/extracting the tarball or zip file is entirely the user responsibility. It is typically done from outside R.

Finally please note that, depending on the size of the data to write to disk and the performance of the disk, `saveHDF5SummarizedExperiment` can take a long time to complete. Use `verbose=TRUE` to see its progress.

`loadHDF5SummarizedExperiment` is generally very fast, even if the assay data is big, because all the assays in the returned object are HDF5Array objects pointing to the on-disk HDF5 datasets located in `dir`. HDF5Array objects are typically light-weight in memory.

### Value

`saveHDF5SummarizedExperiment` returns an invisible SummarizedExperiment object where all the assays are HDF5Array objects pointing to the HDF5 datasets saved in `dir`. It's in fact the same obect as the object that would be returned by calling `loadHDF5SummarizedExperiment` on `dir`.

### Author(s)

Hervé Pagès

### See Also

- SummarizedExperiment and RangedSummarizedExperiment objects in the SummarizedExperiment package.

- The `writeHDF5Array` function which `saveHDF5SummarizedExperiment` uses internally to write the assay data to disk.

### Examples

    library(SummarizedExperiment)
    nrows <- 200; ncols <- 6
    counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
    colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                         row.names=LETTERS[1:6])
    se0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
                                colData=colData)
    se0

    ## Save 'se0' as an HDF5-based SummarizedExperiment object:
    dir <- sub("file", "h5_se0_", tempfile())
    h5_se0 <- saveHDF5SummarizedExperiment(se0, dir)
    h5_se0
    assay(h5_se0, withDimnames=FALSE)  # HDF5Matrix object

    h5_se0b <- loadHDF5SummarizedExperiment(dir)
    h5_se0b
    assay(h5_se0b, withDimnames=FALSE)  # HDF5Matrix object

    ## Sanity checks:
    stopifnot(is(assay(h5_se0, withDimnames=FALSE), "HDF5Matrix"))
    stopifnot(all(DelayedArray(assay(se0)) == assay(h5_se0)))
    stopifnot(is(assay(h5_se0b, withDimnames=FALSE), "HDF5Matrix"))
    stopifnot(all(DelayedArray(assay(se0)) == assay(h5_se0b)))

    ## ---------------------------------------------------------------------
    ## More sanity checks
    ## ---------------------------------------------------------------------

    ## Make a copy of directory 'dir':
    somedir <- sub("file", "somedir", tempfile())
    dir.create(somedir)
    file.copy(dir, somedir, recursive=TRUE)
    dir2 <- list.files(somedir, full.names=TRUE)

    ## 'dir2' contains a copy of 'dir'. Call loadHDF5SummarizedExperiment()
    ## on it.
    h5_se0c <- loadHDF5SummarizedExperiment(dir2)

    stopifnot(is(assay(h5_se0c, withDimnames=FALSE), "HDF5Matrix"))
    stopifnot(all(DelayedArray(assay(se0)) == assay(h5_se0c)))

[Package HDF5Array version 1.10.1 Index]