markziemann / gmea

Gene Methylation Enrichment Analysis
MIT License
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GMEA is too slow #5

Closed markziemann closed 10 months ago

markziemann commented 2 years ago

The current way the test runs is very slow. I think the code could be substantially optimised:

  1. Optimise how the t-stat vals are subset for each gene.
  2. Optimise the wilcox test by re-writing the function to remove unnecessary stuff.
  3. If that is still too slow, we can use C helper code to speed up parts of the process (as done by FGSEA https://www.biorxiv.org/content/10.1101/060012v3)