Load data with rhdf5
Entering edit mode
jose.wo • 0
Last seen 7 months ago

Hello all,

I would like to load data stored in a rhdf5 file. When I try to read the file I get this error:

dataSmillie <- h5read("smillie19_epi.processed.h5ad", "/X/data") Error: Unable to read dataset. Not all required filters available. Missing filters: lzf

I'm not familiar with this package but it seems there is something missing in my R instance. Is this the case or it just means I can't read this data?

Thanks! Jose.

rhdf5 python • 468 views
Entering edit mode
Mike Smith ★ 5.5k
Last seen 8 hours ago
EMBL Heidelberg / de.NBI

This message means the data were compressed with an algorithm (filter in HDF5 terms) that isn't supplied with the standard HDF5 distribution.

I've been working on adding support for extra filters in hdf5filters. It's in the devel branch of Bioconductor, but you can't really use it yet as I haven't added support to rhdf5.

It'd be great if you could open an issue at https://github.com/grimbough/rhdf5 and we can work on getting this integrated. If it's possible for you to share the file that'd also be really helpful.


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