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Reorganize GSEA functions #301

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Reorganize GSEA functions #301

wants to merge 6 commits into from

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yihming
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@yihming yihming commented Jun 3, 2024

Rename fgsea function to gsea, and modify:

  • Add method parameter: default is "blitzgsea"; alternatively support "fgsea"
  • Set min_size to 5, and max_size to 4000
  • For BlitzGSEA method, set symmetric=False, permutations=2000 and center=False by default
  • For fgsea method, rename columns in resulting data frame to match BlitzGSEA result, so that its output could also be used to generate BlitzGSEA plots
  • Only use genes with non-NaN q-values for GSEA
  • In GSEA results, ignore terms with -Inf or Inf NES scores.

Rename write_fgsea_results_to_excel to write_gsea_results_to_excel

@yihming yihming changed the title Gsea Reorganize GSEA functions Jun 3, 2024
@yihming yihming requested a review from bli25 June 3, 2024 02:47
@yihming yihming closed this Jun 7, 2024
@yihming yihming deleted the gsea branch June 11, 2024 18:05
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