search

AlexsLemonade / scpca-docs

User information about ScPCA processing
https://scpca.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
0 stars 1 forks source link

Update sce & merged contents with sample type #252

Closed sjspielman closed 9 months ago

sjspielman commented 9 months ago

From https://github.com/AlexsLemonade/scpca-nf/issues/645#issuecomment-1906731450

Given this, I'm opening up a quick chat for how folks feel about also aiming to get this information into the SCE in the first place; for example, something like metadata(sce)$sample_type <- <"cell line"/"patient-derived xenograft"/"patient tissue">, in the generate_unfiltered_sce area of the code. @allyhawkins @jashapiro

Since we are already reading in the sample metadata in this script, then I would agree that this is a good place to add that information.

We're going to be added a new field into the SCE metadata. This issue tracks documenting it here. Once this is actually implemented in scpca-nf, I'll come back and comment here the specific docs changes we'll need.

sjspielman commented 9 months ago

Noting this doesn't precisely have to do with cell typing, but it has to do with changes that are happening on the same schedule as cell typing. So, I'm adding to that epic.

sjspielman commented 9 months ago

https://github.com/AlexsLemonade/scpca-nf/pull/667 is now completed. The new metadata field sample_type is a character if not multiplex, and it's a named list for each sample if multiplexed. Its values are as shown - https://github.com/AlexsLemonade/scpca-nf/blob/25b599adea91c28e672963577d4f10d77a90b150/bin/generate_unfiltered_sce.R#L186-L190

sjspielman commented 9 months ago

Also, this should go straight into development and then get cherry-picked into sjspielman/celltype-release.

sjspielman commented 9 months ago

All set! Noting this wasn't actually cherry picked since there were also merged_objects.md changes in the same commit, but the relevant matching content was added into sce_file_contents.md.