makeSummarizedExperimentFromLoom {SummarizedExperiment} | R Documentation

## Make a SummarizedExperiment from a '.loom' hdf5 file

### Description

`makeSummarizedExperimentFromLoom` represents a '.loom' file as a `SummarizedExperiment`. The `'/matrix'` and `'/layers'` are represented as `HDF5Array` objects; row and column attributes are parsed to `DataFrame`. Optionally, row or column attributes can be specified as row and and column names.

### Usage

    makeSummarizedExperimentFromLoom(file,
                                     rownames_attr = NULL,
                                     colnames_attr = NULL)

### Arguments

`file` | The path (as a single character string) to the HDF5 file where the dataset is located.
`rownames_attr` | The name of the row attribute to be used as row names.
`colnames_attr` | The name of the column attribute to be used as column names.

### Value

A SummarizedExperiment object with row and column data and one or more assays.

### Author(s)

Martin Morgan

### See Also

http://loompy.org/loompy-docs/format/index.html for a specification of the .loom format.

### Examples

    ## ---------------------------------------------------------------------
    ## BASIC EXAMPLE
    ## ---------------------------------------------------------------------

    file <- system.file(
        package="SummarizedExperiment", "extdata", "example.loom"
    )
    se <- makeSummarizedExperimentFromLoom(file)
    se
    assay(se)
    metadata(se)

[Package SummarizedExperiment version 1.16.1 Index]