Can I visualize individual genes of pathways when running goanna or kegga?
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3.8 years ago
biopat • 0

Hi,

I was running kegga and goana as follows:

> kegga.de=kegga(lrt, species="Mm")

> go <- goana(lrt, species= 'Mm')
> v <- topGO(go, n=100)

For both, the output is a list of pathways that show a number of upregulated, downregulated, or unchanged genes. See below:

Goana Analysis Example

Is there any simple way to visualize which of the genes are actually up or down in these pathways? I have previously used the Desktop version of GSEA by the Broad Institute, which allows nice visualization of these things.

Thank you!

R RNA-Seq • 1.7k views
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The

> v <- topGO(go, n=100)

was actually in run in the next line not as displayed here

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Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

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