[BioC] GO in Bioconductor
jzhang at jimmy.harvard.edu
Thu Jan 5 15:14:20 CET 2006
> Thank you very much for your reply. I would like to know, how to get GOID from
gene name? Is it possible using BioC or I have to do it explicitely?
I would get it from NCBI.
>John Zhang <jzhang at jimmy.harvard.edu> wrote:
>> How can I use Gene Ontology in BioC? Is there any tutorial or manual
>available? Especially how can I construct (extract) a tree if I have a gene
>GO() lists all the environments of the GO package.
>?environment name gives you the description of the environment of interest with
>some example code.
>For the thing you would like to do you may try to get the Gene id for the gene
>(e. g. 19365) and then do the following:
>> goids <- get("19365", GOLOCUSID2GO)
>You will get a few goids the gene maps to. Suppose we are interested in
>GO:0005515 that belongs to MF.
>> get("GO:0005515", GOMFPARENTS) # Get the direct parents
>> get("GO:0005515", GOMFCHILDREN) # Get the direct children
>> get("GO:0005515", GOMFANCESTOR) # Get the parents and grand parents ...
>> get("GO:0005515", GOMFOFFSPRING) # Get the children and grand children ...
>The above do not give you enough to construct a GO tree but you can always
>search the Gene Ontology web site for a tree.
>> Thanks and regards,
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>Department of Medical Oncology
>Dana-Farber Cancer Institute
>44 Binney Street
>Boston, MA 02115-6084
> Ring in the New Year with Photo Calendars. Add photos, events, holidays,
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
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