This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Extracting GSEA gene rankings from gseaResult object

Hello everyone,

I'm currently using clusterProfiler to run GSEA on my samples and I'm interested in seeing the order and ranking of all the genes in my given signature. While the gseaResult object gives me a shortlist of the genes which lead the enrichment of the signature under the core_enrichment column, I was wondering if there was a way to see the ranking and placements of all the genes in the given signature.

Any advice regarding this would be greatly appreciated!

r clusterprofiler gsea
• 1,482 views • link
written by mflab • mflab

1 answer

If you know the set of genes in a given signature you can look at the ranked named statistic you use as the input for GSEA and get their positions, no? Or am I misunderstanding your question

• 0 views • link
written by yura.grabovska • yura.grabovska

Hi Yura,

Thanks for your answer! Indeed, I realized that it's just a matter of looking at the ranked name statistic input - in my case, the logFC.

• 0 views • link
written by mflab • mflab

Log in to answer this question.

More posts like this