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Reorganize GSEA function #305

Merged
merged 7 commits into from
Jun 11, 2024
Merged

Reorganize GSEA function #305

merged 7 commits into from
Jun 11, 2024

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yihming
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@yihming yihming commented Jun 8, 2024

Rename fgsea function to gsea, and modify:

  • Add method parameter: default is "gseapy"; alternatively support "fgsea"
  • For GSEAPy method, use gseapy.prerank function, and rename columns in resulting data frame to match fgsea, so that plot_gsea function and write_gsea_results_to_excel function can work properly
  • Combine de_key and log2fc_key to rank_key, which takes "de_key:attr_key" format so that users don't need to specify 2 parameters
  • Set n_jobs=4 by default
  • Only use genes with non-NaN q-values for GSEA
  • Add verbose parameter for GSEAPy method
  • GSEA results are sorted by padj values in ascending order, then by absolute values of NES scores in descending order, and then by pathway names in dictionary order

Rename write_fgsea_results_to_excel to write_gsea_results_to_excel

@yihming yihming requested a review from bli25 June 8, 2024 08:03
@bli25 bli25 merged commit cbd4b5c into master Jun 11, 2024
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@yihming yihming deleted the add-gseapy branch June 11, 2024 18:04
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2 participants