TENxMatrixSeed-class {HDF5Array} | R Documentation |
TENxMatrixSeed is a low-level helper class that is a direct extension of the 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
TENxMatrix object instead. See ?TENxMatrix
for
more information.
## Constructor function: TENxMatrixSeed(filepath, group="mm10")
filepath, group |
See |
A TENxMatrixSeed object supports the same limited set of methods as
an H5SparseMatrixSeed object. See ?H5SparseMatrixSeed
for the details.
TENxMatrixSeed()
returns a TENxMatrixSeed object.
In order to have access to the full set of operations that are available
for DelayedMatrix objects, a TENxMatrixSeed object
first needs to be wrapped in a DelayedMatrix object,
typically by calling the DelayedArray()
constructor on it.
This is what the TENxMatrix()
constructor function does.
Note that the result of this wrapping is a TENxMatrix object, which is just a TENxMatrixSeed object wrapped in a DelayedMatrix object.
TENxMatrix objects.
H5SparseMatrixSeed objects.
The TENxBrainData
dataset (in the
TENxBrainData package).
h5ls
to list the content of an HDF5 file.
## 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, "mm10") seed path(seed) dim(seed) is_sparse(seed) sparsity(seed) DelayedArray(seed) stopifnot(class(DelayedArray(seed)) == "TENxMatrix")