TENxMatrixSeed-class {HDF5Array} | R Documentation |
TENxMatrixSeed is a low-level helper class for representing a pointer
to an HDF5-based sparse matrix like one used by 10x Genomics for the
1.3 Million Brain Cell Dataset.
TENxMatrixSeed objects are not intended to be used directly. Most
end-users should create and manipulate TENxMatrix objects
instead. See ?TENxMatrix
for more information.
## Constructor function: TENxMatrixSeed(filepath, group="mm10")
filepath, group |
See |
No operation can be performed directly on a TENxMatrixSeed object. It first needs to be wrapped in a DelayedMatrix object. The result of this wrapping is a TENxMatrix object (a TENxMatrix object is just a TENxMatrixSeed object wrapped in a DelayedMatrix object).
TENxMatrixSeed()
returns a TENxMatrixSeed object.
See ?TENxMatrix
for the value returned by sparsity()
and extractNonzeroDataByCol()
.
TENxMatrix objects.
The rhdf5 package on top of which TENxMatrixSeed objects are implemented.
The TENxBrainData
dataset (in the
TENxBrainData package).
## The 1.3 Million Brain Cell Dataset from 10x Genomics is available ## via ExperimentHub: library(ExperimentHub) hub <- ExperimentHub() query(hub, "TENxBrainData") fname <- hub[["EH1039"]] ## The structure of this HDF5 file can be seen using the h5ls() command ## from the rhdf5 package: library(rhdf5) 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: x <- TENxMatrixSeed(fname, "mm10") x path(x) dim(x) sparsity(x)