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\name{H5ADMatrix-class}
\docType{class}
\alias{class:H5ADMatrix}
\alias{H5ADMatrix-class}
\alias{H5ADMatrix}
\alias{DelayedArray,H5ADMatrixSeed-method}
\alias{nzcount,H5ADMatrix-method}
\alias{read_sparse_block,H5ADMatrix-method}
\alias{extractNonzeroDataByCol,H5ADMatrix-method}
\alias{extractNonzeroDataByRow,H5ADMatrix-method}
\title{h5ad central matrices (or matrices in the /layers group)
as DelayedMatrix objects}
\description{
\code{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 \code{X}, of shape #observations x #variables, and
possibly additional data matrices (stored in the HDF5 group \code{/layers})
that share the shape and dimnames of \code{X}.
See \url{https://anndata.readthedocs.io/} for more information.
The H5ADMatrix class is a \link[DelayedArray]{DelayedMatrix} subclass
for representing and operating on the central matrix of an \code{h5ad}
file, or any matrix in its \code{/layers} group.
All the operations available for \link[DelayedArray]{DelayedMatrix}
objects work on H5ADMatrix objects.
}
\usage{
## Constructor function:
H5ADMatrix(filepath, layer=NULL)
}
\arguments{
\item{filepath}{
The path (as a single string) to the \code{h5ad} file.
}
\item{layer}{
\code{NULL} (the default) or the name of a matrix in the \code{/layers}
group. By default (i.e. when \code{layer} is not specified)
\code{H5ADMatrix()} returns the central matrix (\code{X}).
}
}
\value{
\code{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{
\url{https://anndata.readthedocs.io/} for AnnData Python objects
and the \code{h5ad} format.
}
\seealso{
\itemize{
\item \link{HDF5Array} objects for representing conventional (a.k.a.
dense) HDF5 datasets as \link[DelayedArray]{DelayedArray} objects.
\item \link{H5SparseMatrix} objects for representing HDF5 sparse matrices
as \link[DelayedArray]{DelayedMatrix} objects.
\item \link[DelayedArray]{DelayedMatrix} objects in the \pkg{DelayedArray}
package.
\item The \link{H5ADMatrixSeed} helper class.
\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.
\item \link[SparseArray]{SparseArray} objects in the \pkg{SparseArray}
package.
}
}
\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)
\dontrun{
## 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")'
}
}
\keyword{classes}
\keyword{methods}
|
