Geno Ontology Analysis

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Entering edit mode

3.7 years ago

1961012 ▴ 20

I did Gene ontology analysis of DEGs using R Bioconductor as following:

upBP_0.01= new("GOHyperGParams",
             geneIds=selectgenesup,
             universeGeneIds=universegenes,
             annotation="org.Pf.plasmo.db",
             ontology="BP",
             pvalueCutoff=0.01,
             conditional=FALSE,
             testDirection="over")

upBP = hyperGTest(upBP_0.01)

summary(upBP)

and i got the output:

enter image description here `

How can I get the list of genes in each GO term?

Is there any R script for this issue?

How can I visualize them if possible?

Thank you in advance!

GO hypergtest • 1.1k views

ADD COMMENT • link updated 3.7 years ago by h.mon 35k • written 3.7 years ago by 1961012 ▴ 20

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Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.

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ADD REPLY • link 3.7 years ago by Ram 44k

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You forgot to mention you are using the GOstats package.

You can use the mapIds() function from the AnnotationDbi package.

ADD REPLY • link 3.7 years ago by h.mon 35k

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