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Extracting most significant core enrichment genes after performing GSEA

Dear all, I am trying to extract a list of the 10 most significant leading-edge/core enrichment genes after performing GSEA, and visualizing the gene sets with the highest NES, is there any way to do it? I managed to extract a list of leading-edge genes after performing GSEA {clusterProfiler} but the list is quite long (75 genes), so I was trying to find a way to get the 10 most contributing genes. Thank you all so much for your help :)

r gsea
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updated by dthorbur dthorbur • written by biagio.dipietro • biagio.dipietro

10 seems like an arbitrary number. If your analysis indicates there are 75 enriched genes then these should form the basis of downstream analyses (GO/KEGG enrichment, for example). So unless there is a specific reason you need 10, it seems like you're intentionally removing informative data.

By removing outliers without a good reason, you can be accused of cherry picking.

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written by dthorbur dthorbur

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