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rformassspectrometry / QFeatures

Quantitative features for mass spectrometry data
https://RforMassSpectrometry.github.io/QFeatures/
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Robust summary aggregation is very slow for SCP data #123

Open cvanderaa opened 3 years ago

cvanderaa commented 3 years ago

For large data such single-cell proteomics data, the robust summary aggregation is very slow. You can test this with this example:

library(scpdata)
library(scp)
aggregateFeatures(specht2019v3(), 
                  i = "peptides",
                  name = "proteins_rs",
                  fcol = "protein", 
                  fun = MsCoreUtils::robustSummary)

I stopped the run after 1 hour.

lgatto commented 3 years ago

It would be useful to profile the code and identify what chunks take time and why they do (cpu time, memory management, ...).