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
that share the shape and dimnames of
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
file, or any matrix in its
All the operations available for DelayedMatrix objects work on H5ADMatrix objects.
## Constructor function: H5ADMatrix(filepath, layer=NULL)
The path (as a single string) to the
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.
https://anndata.readthedocs.io/ for AnnData Python objects
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.
the zellkonverter package for
h5ad file as/from a
library(zellkonverter) h5ad_file <- system.file("extdata", "krumsiek11.h5ad", package="zellkonverter") X <- H5ADMatrix(h5ad_file) X
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