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martinjzhang / scDRS

Single-cell disease relevance score (scDRS)
https://martinjzhang.github.io/scDRS/
MIT License
98 stars 11 forks source link

Subsetting cells for downstream analysis. #77

Closed jeji0209 closed 7 months ago

jeji0209 commented 7 months ago

Hello. Thank you for the development of this amazing tool. I have one question about conducting the downstream analysis.

Is it statistically acceptable to subset my anndata and full_score.gz file when conducting downstream analysis? The flow I am thinking is:

  1. Run compute-score on my entire dataset to find cell types (e.g. cell type A) that are highly associated with a given trait.
  2. Subset only cell type A cells, and the full_score.gz file of the cells and run perform-downstream, specifically --gene-analysis on the subsetted data to find genes that are correlated with the trait within cell type A.

Thank you in advance :)

martinjzhang commented 7 months ago

Hi, this is statistically valid.