how to do GeneOntology in R using DAVID or other packages to recommed?

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4.7 years ago

Kai_Qi ▴ 130

Hi all:

I have an gene list after analyzing the dynamic expression. I separated them when generating clusters using arbitory numbers, say I generated 3 clusters after trying different numbers, and this cluster is so far satisfying.

I have written the files so I know which gene belongs to which cluster. Now I want to do GeneOntology analysis of the genes in each cluster. Usually, I would extract the genes from the csv files and put them in the DAVID website and then save the files and make it into figures by opening in R again. It is a little bit inconvenient. I am wondering if there any package in R so that i can directly do these steps in R. Consequently, there is no interruption in the code and I can revise the code easily days after if necessary.

Thanks,

RNA-Seq R rna-seq gene • 918 views

ADD COMMENT • link 4.7 years ago by Kai_Qi ▴ 130

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I'd recommend goseq. The example in the vignette assumes you would be working with a well known organism, but if that isn't the case, make sure to pay extra attention to section 6.7.

And I've never tried this before, but this might be helpful/useful also.

ADD REPLY • link 4.7 years ago by Dunois ★ 2.9k

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