Can I visualize individual genes of pathways when running goanna or kegga?

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6.2 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 • 2.0k views

ADD COMMENT • link updated 6.2 years ago by GenoMax 147k • written 6.2 years ago by biopat • 0

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The

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

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

ADD REPLY • link updated 6.2 years ago by GenoMax 147k • written 6.2 years ago by biopat • 0

1

Entering edit mode

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!

ADD REPLY • link 6.2 years ago by GenoMax 147k

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