makeSummarizedExperimentFromLoom: Make a SummarizedExperiment from a '.loom' hdf5 file
In LiNk-NY/SummarizedExperiment: SummarizedExperiment container

Description Usage Arguments Value Author(s) See Also Examples

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.

1
2
3

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

`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.

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

Martin Morgan

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

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

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