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\name{H5ADMatrixSeed-class}
\docType{class}
\alias{class:H5ADMatrixSeed}
\alias{H5ADMatrixSeed-class}
\alias{H5ADMatrixSeed}
\alias{class:Dense_H5ADMatrixSeed}
\alias{Dense_H5ADMatrixSeed-class}
\alias{Dense_H5ADMatrixSeed}
\alias{class:CSC_H5ADMatrixSeed}
\alias{CSC_H5ADMatrixSeed-class}
\alias{CSC_H5ADMatrixSeed}
\alias{class:CSR_H5ADMatrixSeed}
\alias{CSR_H5ADMatrixSeed-class}
\alias{CSR_H5ADMatrixSeed}
\alias{dimnames,Dense_H5ADMatrixSeed-method}
\alias{t.CSC_H5ADMatrixSeed}
\alias{t,CSC_H5ADMatrixSeed-method}
\alias{t.CSR_H5ADMatrixSeed}
\alias{t,CSR_H5ADMatrixSeed-method}
\title{H5ADMatrixSeed objects}
\description{
H5ADMatrixSeed is a low-level helper class used to represent a pointer
to the central matrix stored of an \code{h5ad} file, or to one of the
matrices in the \code{/layers} group.
It is a virtual class with three concrete subclasses: Dense_H5ADMatrixSeed,
CSC_H5ADMatrixSeed, and CSR_H5ADMatrixSeed:
\itemize{
\item The Dense_H5ADMatrixSeed class is used when the matrix is stored
as a conventional HDF5 dataset in the \code{h5ad} file. It is
a direct entension of the \link{HDF5ArraySeed} class.
\item The CSC_H5ADMatrixSeed or CSR_H5ADMatrixSeed classes is used
when the matrix is stored in the \emph{Compressed Sparse Column}
or \emph{Compressed Sparse Row} format in the \code{h5ad} file.
CSC_H5ADMatrixSeed is a direct entension of
\link{CSC_H5SparseMatrixSeed}, and CSR_H5ADMatrixSeed a
direct entension of \link{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
\link{H5ADMatrix} object instead. See \code{?\link{H5ADMatrix}} for
more information.
}
\usage{
## Constructor function:
H5ADMatrixSeed(filepath, layer=NULL)
}
\arguments{
\item{filepath, layer}{
See \code{?\link{H5ADMatrix}} for a description of these arguments.
}
}
\details{
Dense_H5ADMatrixSeed objects support the same limited set of methods as
\link{HDF5ArraySeed} objects, and CSC_H5ADMatrixSeed and CSR_H5ADMatrixSeed
objects support the same limited set of methods as \link{H5SparseMatrixSeed}
objects.
See \code{?\link{HDF5ArraySeed}} and \code{?\link{H5SparseMatrixSeed}}
for the details.
}
\value{
\code{H5ADMatrixSeed()} returns an H5ADMatrixSeed derivative
(Dense_H5ADMatrixSeed or CSC_H5ADMatrixSeed or CSR_H5ADMatrixSeed)
of shape #variables x #observations.
}
\section{H5ADMatrixSeed vs H5ADMatrix objects}{
In order to have access to the full set of operations that are available
for \link[DelayedArray]{DelayedMatrix} objects, an H5ADMatrixSeed
derivative first needs to be wrapped in a \link[DelayedArray]{DelayedMatrix}
object, typically by calling the \code{\link[DelayedArray]{DelayedArray}()}
constructor on it.
This is what the \code{\link{H5ADMatrix}()} constructor function does.
Note that the result of this wrapping is an \link{H5ADMatrix} object,
which is just an H5ADMatrixSeed derivative wrapped in a
\link[DelayedArray]{DelayedMatrix} object.
}
\references{
\url{https://anndata.readthedocs.io/} for AnnData Python objects
and the \code{h5ad} format.
}
\seealso{
\itemize{
\item \link{H5ADMatrix} objects.
\item \link{HDF5ArraySeed} and \link{H5SparseMatrixSeed} objects.
\item \code{\link[zellkonverter]{readH5AD}} and
\code{\link[zellkonverter]{writeH5AD}} in
the \pkg{zellkonverter} package for
importing/exporting an \code{h5ad} file as/from a
\link[SingleCellExperiment]{SingleCellExperiment} object.
}
}
\examples{
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")
}
\keyword{classes}
\keyword{methods}
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