Can I run calcNhoodDistance before countCells

[yulijia]

Hi

Thanks for creating the great package. I am currently applying MiloR to a large dataset with multiple design matrices. I've noticed that the "calcNhoodDistance" step is quite time-consuming. I would like to know if it's possible to run "calcNhoodDistance" before "countCells" so that I can save the object after calculating the neighborhood distances and then proceed with the remaining steps using multiple design matrices.

[emdann]

Hi @yulijia, You can avoid using calcNhoodDistance by using the new graph-only mode, by setting refinement_scheme="graph" in makeNhoods and fdr.weighting="graph-overlap" in testNhoods. This should make your analysis significantly faster. See quickstart example here.

[yulijia]

Hi @emdann
Thank!
If I still use the old mode, can I know if I can run calcNhoodDistance before countCells?

[DarioS]

Also, it doesn't respond to R terminal interrupt or Linux kill signal unless I do kill -9. Please allow interrupts.