[BioC] Creating annotation database for GOstat

[James W. MacDonald]

Hi Naomi,

http://bioconductor.org/packages/2.11/bioc/vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf

Best,

Jim



On 2/4/2013 10:13 PM, naomi at stat.psu.edu wrote:
> I have a data base with gene names and GO annotation for maize.  Having
> selected a gene list, I want to get this annotation file into R in a
> format that allows me to run GOstat.  I am not sure how to proceed.  A
> sample of the annotation file is below.
>
> GRMZM2G026396,,
> GRMZM2G160606,5737,cytoplasm
> GRMZM2G103702,,
> GRMZM5G810061,3924,GTPase activity
> GRMZM5G810061,5525,GTP binding
> GRMZM2G019356,,
> GRMZM2G032655,,
> GRMZM2G098423,51287,NAD binding
> GRMZM2G136395,,
> GRMZM2G137676,30599,pectinesterase activity
> GRMZM2G137676,42545,cell wall modification
> GRMZM2G137676,5618,cell wall
>
> Thanks for any assistance.  A pointer to the correct vignette or manual
> should be enough.
>
> Naomi Altman
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099