Closed sjspielman closed 1 month ago
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.
Closed by #779
Relevant discussions
https://github.com/AlexsLemonade/OpenScPCA-analysis/discussions/727 & https://github.com/AlexsLemonade/OpenScPCA-analysis/discussions/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 usebluster::bootstrapStability
for this, settingcompare=pairwiseRand
(or hey, evencompare=Jaccard
- we can make this an option).