[BioC] gene count in a GO term

[James W. MacDonald]

Hi Tao,

Shi, Tao wrote:
> Hi list,
> 
> Please forgive if this was asked before.
> 
> In R, is there a way to find out how many Human gene products in a GO
> term (including all its children) like those reported in AmiGo?  I'm
> talking about ALL the gene products, not just those on a affy chip.
> For example, for GO:0005921 and children and its children, the number
> is 6.

There are only 6 if you restrict to TAS and IDA. If you allow IEA then 
there are 27:

 > library(org.Hs.eg.db)
 > get("GO:0005921", org.Hs.egGO2ALLEGS)
         TAS         TAS         IEA         IEA         IEA         TAS
      "1823"      "2697"      "2700"      "2701"      "2702"      "2703"
         TAS         TAS         IEA         IEA         IEA         IEA
      "2705"      "2706"      "2707"      "2709"      "4284"      "9742"
         IEA         IEA         IEA         IEA         IEA         IEA
     "10052"     "10804"     "24145"     "56666"     "57165"     "57369"
         IEA         IEA         IEA         IDA         IEA         IEA
     "81025"     "84694"    "116337"    "125111"    "127534"    "219770"
         IEA         IEA         IEA
    "349149"    "375519" "100126572"


Best,

Jim


> 
> Many thanks!
> 
> ...Tao
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662