H5ADMatrixSeed is a low-level helper class used to represent a pointer
to the central matrix stored of an
h5ad file, or to one of the
matrices in the
It is a virtual class with three concrete subclasses: Dense_H5ADMatrixSeed, CSC_H5ADMatrixSeed, and CSR_H5ADMatrixSeed:
The Dense_H5ADMatrixSeed class is used when the matrix is stored
as a conventional HDF5 dataset in the
h5ad file. It is
a direct entension of the HDF5ArraySeed class.
The CSC_H5ADMatrixSeed or CSR_H5ADMatrixSeed classes is used
when the matrix is stored in the Compressed Sparse Column
or Compressed Sparse Row format in the
CSC_H5ADMatrixSeed is a direct entension of
CSC_H5SparseMatrixSeed, and CSR_H5ADMatrixSeed a
direct entension of CSR_H5SparseMatrixSeed.
Note that an H5ADMatrixSeed derivative is not intended to be used directly.
Most end users will typically create and manipulate a higher-level
H5ADMatrix object instead. See
## Constructor function: H5ADMatrixSeed(filepath, layer=NULL)
Dense_H5ADMatrixSeed objects support the same limited set of methods as
HDF5ArraySeed objects, and CSC_H5ADMatrixSeed and CSR_H5ADMatrixSeed
objects support the same limited set of methods as H5SparseMatrixSeed
for the details.
H5ADMatrixSeed() returns an H5ADMatrixSeed derivative
(Dense_H5ADMatrixSeed or CSC_H5ADMatrixSeed or CSR_H5ADMatrixSeed)
of shape #variables x #observations.
In order to have access to the full set of operations that are available
for DelayedMatrix objects, an H5ADMatrixSeed
derivative first needs to be wrapped in a DelayedMatrix
object, typically by calling the
constructor on it.
This is what the
H5ADMatrix() constructor function does.
Note that the result of this wrapping is an H5ADMatrix object, which is just an H5ADMatrixSeed derivative wrapped in a DelayedMatrix object.
https://anndata.readthedocs.io/ for AnnData Python objects
HDF5ArraySeed and H5SparseMatrixSeed objects.
the zellkonverter package for
h5ad file as/from a
library(zellkonverter) h5ad_file <- system.file("extdata", "krumsiek11.h5ad", package="zellkonverter") seed <- H5ADMatrixSeed(h5ad_file) seed path(seed) dim(seed) is_sparse(seed) DelayedArray(seed) stopifnot(class(DelayedArray(seed)) == "H5ADMatrix")
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