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.

Sign up for GitHub

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

Jump to bottom

rOpenScPCA: function to calculate stability #773

Closed
sjspielman opened this issue Sep 20, 2024 · 2 comments
Closed

rOpenScPCA: function to calculate stability #773

sjspielman opened this issue Sep 20, 2024 · 2 comments
Assignees
@sjspielman
Labels
analysis

Comments

@sjspielman
Copy link
Member

sjspielman commented Sep 20, 2024 •
edited
Loading

Relevant discussions

#727 & #731

Proposed addition

This issue tracks adding a function and associated tests to rOpenScpCA to calculate stability via bootstrapping & ARI** from a given set of clusters. The function should take a PC matrix (or sce/seurat object) and data frame with clusters and cell IDs. We should be able to directly use bluster::bootstrapStability for this, setting compare=pairwiseRand (or hey, even compare=Jaccard - we can make this an option).
@sjspielman sjspielman self-assigned this Sep 20, 2024
@sjspielman
Copy link
Member Author

Disappointingly, seems like the bluster function won't work for us (I bet this is something we once figured out but before I joined the data lab...), since it returns only the average or median of the bootstrapped values, not a value for each bootstrap iteration itself.

@sjspielman sjspielman mentioned this issue Sep 24, 2024
Merged
@sjspielman
Copy link
Member Author

Closed by #779

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@sjspielman sjspielman

Labels
analysis
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@sjspielman