TENxMatrixSeed-class {HDF5Array} | R Documentation

## TENxMatrixSeed objects

### Description

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.

### Usage

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

### Arguments

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

### Details

A TENxMatrixSeed object supports the same limited set of methods as an H5SparseMatrixSeed object. See `?H5SparseMatrixSeed` for the details.

### Value

`TENxMatrixSeed()` returns a TENxMatrixSeed object.

### TENxMatrixSeed vs TENxMatrix objects

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.

### See Also

- TENxMatrix objects.

- H5SparseMatrixSeed objects.

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

- `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, "mm10")
    seed
    path(seed)
    dim(seed)
    is_sparse(seed)
    sparsity(seed)

    DelayedArray(seed)
    stopifnot(class(DelayedArray(seed)) == "TENxMatrix")

[Package HDF5Array version 1.20.0 Index]