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Configure functional enrichment to work with GSEA #424

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b-full opened this issue Dec 13, 2024 · 0 comments
Open

Configure functional enrichment to work with GSEA #424

b-full opened this issue Dec 13, 2024 · 0 comments

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@b-full
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b-full commented Dec 13, 2024

In lib/lcdbwf/R/functional-enrichment.R, enrich_test() at line 127 has "OR" (Over Representation Analysis) hardcoded as a default parameter and in fact never uses the value assigned in the config.yaml file. We want to be able to use "GSEA"(Gene Set Enrichment Analysis) as well by assigning it in config.yaml, but it seems setting kind=GSEA currently throws an error. We need to configure this to work with both kind=OR as well as kind=GSEA.

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