H5ADMatrix-class {HDF5Array} | R Documentation

## h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects

### Description

`h5ad` files are HDF5 files used for on-disk representation of AnnData Python objects. At the very minimum, they contain a central data matrix, named `X`, of shape #observations x #variables, and possibly additional data matrices (stored in the HDF5 group `/layers`) that share the shape and dimnames of `X`. See https://anndata.readthedocs.io/ for more information.

The H5ADMatrix class is a DelayedMatrix subclass for representing and operating on the central matrix of an `h5ad` file, or any matrix in its `/layers` group.

All the operations available for DelayedMatrix objects work on H5ADMatrix objects.

### Usage

    ## Constructor function:
    H5ADMatrix(filepath, layer=NULL)

### Arguments

`filepath` | The path (as a single string) to the `h5ad` file.
`layer` | `NULL` (the default) or the name of a matrix in the `/layers` group. By default (i.e. when `layer` is not specified) `H5ADMatrix()` returns the central matrix (`X`).

### Value

`H5ADMatrix()` returns an H5ADMatrix object of shape #variables x #observations. Note that in Python and HDF5 the shape of this matrix is considered to be #observations x #variables, but in R it is transposed. This follows the widely adopted convention of transposing HDF5 matrices when they get loaded into R.

### References

https://anndata.readthedocs.io/ for AnnData Python objects and the `h5ad` format.

### See Also

- HDF5Array objects for representing conventional (a.k.a. dense) HDF5 datasets as DelayedArray objects.

- H5SparseMatrix objects for representing HDF5 sparse matrices as DelayedMatrix objects.

- DelayedMatrix objects in the DelayedArray package.

- The H5ADMatrixSeed helper class.

- `readH5AD` and `writeH5AD` in the zellkonverter package for importing/exporting an `h5ad` file as/from a SingleCellExperiment object.

### Examples

    library(zellkonverter)
    h5ad_file <- system.file("extdata", "krumsiek11.h5ad",
                             package="zellkonverter")
    X <- H5ADMatrix(h5ad_file)
    X

[Package HDF5Array version 1.20.0 Index]