SummarizedExperiment: makeSummarizedExperimentFromLoom – R documentation

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makeSummarizedExperimentFromLoom

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

Examples

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

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

SummarizedExperiment

SummarizedExperiment container

v1.20.0

Artistic-2.0

Authors

Martin Morgan, Valerie Obenchain, Jim Hester, Hervé Pagès

Initial release