search

AlexsLemonade / OpenScPCA-analysis

An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal
Other
9 stars 17 forks source link

rOpenScPCA: function to calculate stability #773

Closed sjspielman closed 1 month ago

sjspielman commented 1 month ago

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 use bluster::bootstrapStability for this, setting compare=pairwiseRand (or hey, even compare=Jaccard - we can make this an option).

sjspielman commented 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.

sjspielman commented 1 month ago

Closed by #779