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\name{TENxMatrixSeed-class}
\docType{class}
\alias{class:TENxMatrixSeed}
\alias{TENxMatrixSeed-class}
\alias{TENxMatrixSeed}
\title{TENxMatrixSeed objects}
\description{
TENxMatrixSeed is a low-level helper class that is a direct extension
of the \link{H5SparseMatrixSeed} class. It is used to represent a
pointer to an HDF5 sparse matrix that is stored in the CSR/CSC/Yale
format ("Compressed Sparse Row") and follows the 10x Genomics convention
for storing the dimensions of the matrix.
Note that a TENxMatrixSeed object is not intended to be used directly.
Most end users will typically create and manipulate a higher-level
\link{TENxMatrix} object instead. See \code{?\link{TENxMatrix}} for
more information.
}
\usage{
## Constructor function:
TENxMatrixSeed(filepath, group="matrix")
}
\arguments{
\item{filepath, group}{
See \code{?\link{TENxMatrix}} for a description of these arguments.
}
}
\details{
A TENxMatrixSeed object supports the same limited set of methods as
an \link{H5SparseMatrixSeed} object. See \code{?\link{H5SparseMatrixSeed}}
for the details.
}
\value{
\code{TENxMatrixSeed()} returns a TENxMatrixSeed object.
}
\section{TENxMatrixSeed vs TENxMatrix objects}{
In order to have access to the full set of operations that are available
for \link[DelayedArray]{DelayedMatrix} objects, a TENxMatrixSeed object
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{TENxMatrix}()} constructor function does.
Note that the result of this wrapping is a \link{TENxMatrix} object,
which is just a TENxMatrixSeed object wrapped in a
\link[DelayedArray]{DelayedMatrix} object.
}
\seealso{
\itemize{
\item \link{TENxMatrix} objects.
\item \link{H5SparseMatrixSeed} objects.
\item The \code{\link[TENxBrainData]{TENxBrainData}} dataset (in the
\pkg{TENxBrainData} package).
\item \code{\link{h5ls}} to list the content of an HDF5 file.
}
}
\examples{
## The 1.3 Million Brain Cell Dataset from 10x Genomics is available
## via ExperimentHub:
library(ExperimentHub)
hub <- ExperimentHub()
query(hub, "TENxBrainData")
fname <- hub[["EH1039"]]
## 'fname' is an HDF5 file. Use h5ls() to list its content:
h5ls(fname)
## The 1.3 Million Brain Cell Dataset is represented by the "mm10"
## group. We point the TENxMatrixSeed() constructor to this group
## to create a TENxMatrixSeed object representing the dataset:
seed <- TENxMatrixSeed(fname, group="mm10")
seed
path(seed)
dim(seed)
is_sparse(seed)
sparsity(seed)
DelayedArray(seed)
stopifnot(class(DelayedArray(seed)) == "TENxMatrix")
}
\keyword{classes}
\keyword{methods}
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