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AlexsLemonade / scpca-docs

User information about ScPCA processing
https://scpca.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Include description of sample metadata present in SCE object #154

Closed allyhawkins closed 1 year ago

allyhawkins commented 1 year ago

Closes #146 Stacked on #153

This PR modifies the current SCE contents to include a table listing all of the sample metadata columns that are present in metadata(sce)$sample_metadata. I added a row for listing the sample_metadata in the table with the metadata(sce) contents, but then I also made a separate section just for the sample metadata. Here, I added a table showing the expected columns in the sample metadata table that's stored in the object. I also added a note that there may be additional columns depending on the project.

I added in the seq_unit and assay_ontology_term_id to the metadata list since those had not been added yet.

While working on this, I also removed the note about participant_id only being filled in for participants that contain multiple samples. Those are now present for all of our samples.

allyhawkins commented 1 year ago

@jashapiro thanks for catching those link inconsistencies! I believe I got all of them, but let me know if I missed one. I think the only thing left is to decide if we are keeping the donor_id or changing back to participant_id.