[BioC] GO annotation
Srinivasan, Sathish K
SSrinivasan at med.miami.edu
Sat Sep 22 07:21:29 CEST 2012
Could you suggest a go-to literature reference on annotating genomic data using bioconductor packages, probably a book or any of its kind. Thanks
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Marc Carlson
Sent: Friday, September 21, 2012 8:49 PM
To: bioconductor at r-project.org
Subject: Re: [BioC] GO annotation
First of all it all depends on what you have for gene identifiers. If you are like most people you will have entrez gene IDs. So for now I will assume you have those.
## So lets further assume you are working with humans and just choose the 1st two entrez gene IDs so that we can make a (hopefully meaningful) example ids = c("1","2") ## now load the org library for humans
## then you can call select to extract your GO IDs like this:
select(org.Hs.eg.db, keys = ids, cols = "GO", keytype = "ENTREZID")
Now one thing to notice is that if you have some other kind of identifier, then your keytype argument will have to be set to a different value. And hopefully, the kind of ID you are using, is present in the package that you have to search... See the manual page for select for more information.
From your question, I also recognize that you may not be able to do this because it sounds like you might be using a more unusual organism and not be using something commonplace like human. Well don't give up just yet, because we may be able to help you there too. You can look at the manual page for the function makeOrgPackageFromNCBI to learn how you can try to generate an org package from just the taxonomy ID (which you can look up on NCBIs website). If the data is available at NCBI, then you should be able to generate a package from NCBI that will match your organism of choice.
Does that answer your question?
On 09/21/2012 02:35 AM, KJ Lim wrote:
> Dear Bioconductor community,
> Good day.
> I did the differential expression analysis for my RNA-Seq data with
> edgeR package. I have a list of differentially expressed genes now and
> I would like to find the GO terms for the genes.
> I have been reading and searching around for the right package. But, I
> found that several packages are developed based on model species.
> Could the community kindly please suggest me what GO annotation
> package I can use for non-model species; plant RNA-Seq data?
> Thank you very much and have a nice weekend.
> Best regards,
> KJ Lim
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