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YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
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What is the meaning of geneRatio for dotplot of KEGG GSEA enrichment result #364

Open liuxianghui opened 3 years ago

liuxianghui commented 3 years ago

Just a simple question, when we use dotplot to look at the enrichment results, x axis is Gene Ratio.
for enrichKEGG result, I can understand, there are GeneRatio and BgRatio columns there. However, when you look at the gseKEGG results ( GSEA), how are Gene Ratio calculated? I noticed that in the results, there is no such column of Gene Ratio... but the dotplot did use a value to plot... Please kindly suggest,

huerqiang commented 3 years ago

The geneRatio in gseKEGG results is calculated by dotplot. The calculation method is : (count of core enrichment genes) / (count of pathway genes) .

liuxianghui commented 3 years ago

Thank you.

liuxianghui commented 3 years ago

I have one more question. I am curious to know that since dotplot can be used to plot gseKEGG results. Why in compareclusters, this function gseKEGG is not added to the four functions available. Now we can only do compareclusters for multiple over representation analysis results, why can apply to GSEA results?