Understanding "gene ratio" when using plotEnrich(c())
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marinaw ▴ 20
@9c8b15cf
Last seen 28 days ago
Canada

Hi all,

I've been using the function enrichr(c(). The output is exactly what I wanted (for my purposes) but I have one question regarding the plotEnrich(c()) function:

you can plot the output either as y = count or y = ratio. What is the gene ratio here exactly? I can't seem to find a clear answer for this. Is it the number of genes in your data that are found in a particular gene set, then divided by the total number of genes in that gene set (the gene set coming from the library/database you selected)?

Thanks!

plotEnrich enrichr • 1.2k views
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ATpoint ★ 3.9k
@atpoint-13662
Last seen 22 minutes ago
Germany

enrichR is not a Bioconductor package. My best guess though based on the source code https://github.com/wjawaid/enrichR/blob/master/R/functions.R#L381 is that it is the ratio for signifcant genes vs all annotated genes per pathway. So for example a pathway/term had 50 annotated genes and 10 of these are among your list of genes you give to the enrichment analysis, then it would be 10/50. That is quite common to report in these sorts of analysis. It could also be called 'term coverage' imo.

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Ah, I apologize. Thank you for the insight regardless!

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