TENxMatrixSeed-class {HDF5Array} | R Documentation

## TENxMatrixSeed objects

### Description

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.

### Usage

    ## Constructor function:
    TENxMatrixSeed(filepath, group="mm10")

### Arguments

`filepath, group` | See `?TENxMatrix` for a description of these arguments.

### Details

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).

### Value

`TENxMatrixSeed()` returns a TENxMatrixSeed object.

See `?TENxMatrix` for the value returned by `sparsity()` and `extractNonzeroDataByCol()`.

### See Also

- TENxMatrix objects.

- The rhdf5 package on top of which TENxMatrixSeed objects are implemented.

- The `TENxBrainData` dataset (in the TENxBrainData package).

### 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"]]

    ## 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)

[Package HDF5Array version 1.12.3 Index]