Gene Annotation after EdgeR in R

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2.7 years ago

saamar.rajput ▴ 80

Dear All,

I have an EdgeR analysis for Human genes. Now I want to add the annotation for all individual genes in a column against the genes. Is there a package in R that takes a list of genes and generates the annotation against each gene?

Thank you in advance!

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ADD COMMENT • link updated 2.7 years ago by ATpoint 85k • written 2.7 years ago by saamar.rajput ▴ 80

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What do you mean by "annotate"? If you want functonal enrichment check the gprofiler2 package or its GUI:

https://biit.cs.ut.ee/gprofiler/gost

https://cran.r-project.org/web/packages/gprofiler2/index.html

ADD REPLY • link 2.7 years ago by ATpoint 85k

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I am sorry it was not clear enough, but i want functional annotation for every single gene. Like what is the function of this one gene, i want this for a list of genes.

ADD REPLY • link 2.7 years ago by saamar.rajput ▴ 80

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This does not exist I think in the way you imagine it. You cannot enrich a single gene for anything, and a gene's function can be diverse depending on cellular context. You can pull out simple gene descriptions with tools like biomaRt, but for enriched terms you need to provide gene lists that then are to be compared to annotated pathways and processes. After all there is manual literature work to be done to interpret your results.

ADD REPLY • link 2.7 years ago by ATpoint 85k

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