,
Ilia Kats [aut] | Title: | Serialization for MultiAssayExperiment Objects |
|---|---|
| Description: | Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an HDF5-based format for data storage. |
| Authors: | Danila Bredikhin [aut, cre] ,
Ilia Kats [aut] |
| Maintainer: | Danila Bredikhin <[email protected]> |
| License: | GPL-3 |
| Version: | 1.9.0 |
| Built: | 2024-07-02 05:23:33 UTC |
| Source: | https://github.com/bioc/MuData |
SingleCellExperiment.In file-backed mode, the main X matrix is not read into memory,
but references the HDF5 file and its required parts are read on demand.
This requires the HDF5Array package to be installed.
readH5AD(file, backed = FALSE)readH5AD(file, backed = FALSE)
file |
Path to the .h5ad file. |
backed |
Whether to use file-backed mode. |
data(miniACC, package="MultiAssayExperiment") writeH5AD(miniACC[[1]], "miniacc.h5ad") sce <- readH5AD("miniacc.h5ad")data(miniACC, package="MultiAssayExperiment") writeH5AD(miniACC[[1]], "miniacc.h5ad") sce <- readH5AD("miniacc.h5ad")
MultiAssayExperiment.In file-backed mode, the main X matrices are not read into memory,
but reference the HDF5 file and their required parts are read on demand.
This requires the HDF5Array package to be installed.
readH5MU(file, backed = FALSE)readH5MU(file, backed = FALSE)
file |
Path to the .h5mu file. |
backed |
Whether to use file-backed mode. |
data(miniACC, package="MultiAssayExperiment") writeH5MU(miniACC, "miniacc.h5mu") mae <- readH5MU("miniacc.h5mu")data(miniACC, package="MultiAssayExperiment") writeH5MU(miniACC, "miniacc.h5mu") mae <- readH5MU("miniacc.h5mu")
Note that NA values are not supported by HDF5, and therefore by h5ad. The behavior of this function if NAs are present is undefined.
writeH5AD(object, file, overwrite)writeH5AD(object, file, overwrite)
object |
The object to save. |
file |
Name of the file to save to. |
overwrite |
Currently unused. |
NULL, invisibly
data(miniACC, package="MultiAssayExperiment") writeH5AD(miniACC[[1]], "miniacc.h5ad")data(miniACC, package="MultiAssayExperiment") writeH5AD(miniACC[[1]], "miniacc.h5ad")
MultiAssayExperiment to an .h5mu file.Note that NA values are not supported by HDF5, and therefore by h5mu. The behavior of this function if NAs are present is undefined.
writeH5MU(object, file, overwrite)writeH5MU(object, file, overwrite)
object |
|
file |
Name of the file to save to. |
overwrite |
Currently unused. |
NULL, invisibly
data(miniACC, package="MultiAssayExperiment") writeH5MU(miniACC, "miniacc.h5mu")data(miniACC, package="MultiAssayExperiment") writeH5MU(miniACC, "miniacc.h5mu")