HDF5Array: HDF5 datasets as array-like objects in R

H5ADMatrix-class

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.

Examples

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

class(X)  # H5ADMatrix
is(X, "DelayedMatrix")  # TRUE

class(seed(X))  # Dense_H5ADMatrixSeed

dim(X)
path(X)
is_sparse(X)  # FALSE

## Use coercion to load the full dataset into memory:
as.matrix(X)          # as ordinary array (usually not recommended)

## Not run: 
  ## Works only if H5ADMatrix object is sparse!
  as(X, "dgCMatrix")    # as dgCMatrix
  as(X, "SparseArray")  # as SparseArray object (most efficient)
  SparseArray(X)        # equivalent to 'as(X, "SparseArray")'

## End(Not run)

Bioconductor/HDF5Array documentation built on Nov. 30, 2024, 3:14 a.m.