Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add support for seurat hdf5 format. #59

Open
wants to merge 2 commits into
base: devel
Choose a base branch
from

Conversation

yduanBioinfo
Copy link

Add support for h5seurat format to TENxMatrix object. In this version, only functions in TENxMatrix-class and TENxMatrixSeed-class has been changed. At the same time, I have added a toy data and written some example codes in the help document.

As a concern, the change in .find_rownames_dataset of TENxMatrixSeed-class is a little dangerous. I'm afraid that the 'features' prior than 'features/id' will cause a bug. However, if set 'feature/id' prior, it will cause an error: "Error in H5Lexists(fid, name) : HDF5. Links. Can't get value".
If the bug actually exist, it's maybe a solution to write a new function .read_h5seurat_component to read h5seurat data separately as in my last pull request.

@hpages
Copy link
Contributor

hpages commented Nov 1, 2023

Thanks @yduanBioinfo. Will look at this shortly.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants