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\name{H5SparseMatrix-class}
\docType{class}
\alias{class:H5SparseMatrix}
\alias{H5SparseMatrix-class}
\alias{H5SparseMatrix}
\alias{DelayedArray,H5SparseMatrixSeed-method}
\alias{nzcount,H5SparseMatrix-method}
\alias{read_sparse_block,H5SparseMatrix-method}
\alias{extractNonzeroDataByCol,H5SparseMatrix-method}
\alias{extractNonzeroDataByRow,H5SparseMatrix-method}
\title{HDF5 sparse matrices as DelayedMatrix objects}
\description{
The H5SparseMatrix class is a \link[DelayedArray]{DelayedMatrix} subclass
for representing and operating on an HDF5 sparse matrix stored in
CSR/CSC/Yale format.
All the operations available for \link[DelayedArray]{DelayedMatrix}
objects work on H5SparseMatrix objects.
}
\usage{
## Constructor function:
H5SparseMatrix(filepath, group)
}
\arguments{
\item{filepath}{
The path (as a single string) to the HDF5 file (\code{.h5} or
\code{.h5ad}) where the sparse matrix is located.
}
\item{group}{
The name of the group in the HDF5 file where the sparse matrix is stored.
}
}
\value{
An H5SparseMatrix object.
}
\seealso{
\itemize{
\item \link{HDF5Array} objects for representing conventional (a.k.a.
dense) HDF5 datasets as \link[DelayedArray]{DelayedArray} objects.
\item \link{H5ADMatrix} objects for representing h5ad central
matrices (or matrices in the \code{/layers} group)
as \link[DelayedArray]{DelayedMatrix} objects.
\item \link{TENxMatrix} objects for representing 10x Genomics
datasets as \link[DelayedArray]{DelayedMatrix} objects.
\item \link[DelayedArray]{DelayedMatrix} objects in the \pkg{DelayedArray}
package.
\item The \link{H5SparseMatrixSeed} helper class.
\item \code{\link{h5ls}} to list the content of an HDF5 file (\code{.h5}
or \code{.h5ad}).
\item \link[SparseArray]{SparseArray} objects in the \pkg{SparseArray}
package.
}
}
\examples{
library(zellkonverter)
h5ad_file <- system.file("extdata", "example_anndata.h5ad",
package="zellkonverter")
rhdf5::h5ls(h5ad_file)
M <- H5SparseMatrix(h5ad_file, "/obsp/connectivities")
M
class(M) # H5SparseMatrix
is(M, "DelayedMatrix") # TRUE
seed(M)
class(seed(M)) # CSC_H5SparseMatrixSeed
dim(M)
path(M)
is_sparse(M) # TRUE
## Use coercion to load the full dataset into memory:
as.matrix(M) # as ordinary array (usually not recommended)
as(M, "dgCMatrix") # as dgCMatrix
as(M, "SparseArray") # as SparseArray object (most efficient)
SparseArray(M) # equivalent to 'as(M, "SparseArray")'
}
\keyword{classes}
\keyword{methods}
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