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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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RunDynamicFeatures runtime #207

Open france-hub opened 8 months ago

france-hub commented 8 months ago

Hello!

Thanks for the package and nice visualizations!

I am trying to run RunDynamicFeatures and would like to ask what's the expected runtime. I think the function fits GAM similar to what tradeSeq does; however, fitGAM from TradeSeq takes ~25 min to be fitted on my machine. I tried RunDynamicFeatures on the same subset, same machine and it has been stuck on this: Number of candidate features(union): 241 Calculate dynamic features for Lineage1...

for 12 hours now.

I tried on an object of 10k features and 21k cells and now on a subset of 2k features (selected by approximate multinomial deviance) and 21k cells. This is the code line I am using:

cd8.sub <- RunDynamicFeatures(srt = cd8.sub, lineages = c("Lineage1", "Lineage2"), n_candidates = 200, BPPARAM = BiocParallel::MulticoreParam(workers = 10))

Is this runtime expected?

Thank you for your help!

Best, Francesco

nbutyrate commented 3 months ago

hi france-hub,

were you able to solve this issue? any idea how to speed this up?