[BioC] GO terms

[Wolfgang Huber]

Hi Michael

another way of doing that is

	tt = toTable(GOTERM)

Best wishes
	Wolfgang	

  watson (IAH-C) scripsit 02/16/2010 10:27 AM:
> I have no idea if this helps, but the first thing I do with GO.db is turn it into a data.frame.
> I realise this loses the hierarchical structure, but it is invaluable if you want to use functions such as merge().
> 
> library(GO.db)
> xx <- as.list(GOTERM)
> foo <- function(x) c(GOID(x), Term(x),Definition(x), Ontology(x))
> gomat <- t(sapply(xx, foo, simplify=TRUE))
> gomat <- as.data.frame(gomat)
> colnames(gomat) <- c("ID","Term","Definition","Ontology")
> 
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Heidi Dvinge
> Sent: 16 February 2010 00:15
> To: Adrian Johnson
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] GO terms
> 
> Hello Adrian,
> 
> could you perhaps provide your sessionInfo? When I use the examples
> provide on probeSetSummary in GOstats to create an object called ps, I can
> then say:
> 
>> ps[1]
> $`GO:0043412`
>     EntrezID ProbeSetID selected
> 1      10114     102_at        1
> 2      10114   41501_at        0
> 3      10114   41502_at        0
> 4      10152  1040_s_at        1
> 5      10152   135_g_at        0
> ...
> 
>> names(ps)[1:10]
>  [1] "GO:0043412" "GO:0006796" "GO:0006468" "GO:0044267" "GO:0044260"
> "GO:0042221" "GO:0002520"
>  [8] "GO:0045321" "GO:0044419" "GO:0030097"
>> Term(names(ps)[1:10])
>                                   GO:0043412                              
>     GO:0006796
>                    "biopolymer modification"                "phosphate
> metabolic process"
>                                   GO:0006468                              
>     GO:0044267
>         "protein amino acid phosphorylation"         "cellular protein
> metabolic process"
>                                   GO:0044260                              
>     GO:0042221
>   "cellular macromolecule metabolic process"              "response to
> chemical stimulus"
>                                   GO:0002520                              
>     GO:0045321
>                  "immune system development"                      
> "leukocyte activation"
>                                   GO:0044419                              
>     GO:0030097
> "interspecies interaction between organisms"                              
>  "hemopoiesis"
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-apple-darwin8.11.1
> 
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
>  [1] GO.db_2.3.5         GOstats_2.12.0      graph_1.24.0       
> Category_2.12.0     annotate_1.24.0
>  [6] hgu95av2.db_2.3.5   org.Hs.eg.db_2.3.6  RSQLite_0.7-3       DBI_0.2-4
>           AnnotationDbi_1.8.0
> [11] affy_1.24.0         Biobase_2.6.0
> 
> loaded via a namespace (and not attached):
>  [1] affyio_1.14.0        genefilter_1.28.0    GSEABase_1.8.0      
> preprocessCore_1.8.0
>  [5] RBGL_1.22.0          splines_2.10.0       survival_2.35-7     
> tools_2.10.0
>  [9] XML_2.6-0            xtable_1.5-5
> 
> 
> 
>> Hi Heidi,
>> Thanks for quick reply.
>> It doesnt work for me. Although GOTERMS$"GO:ID" works.
>>
>> I have all my GOIDs in a list, I want to get the terms for that IDs in
>> character vector.
>>
>>
>>> Term("GO:0006916")
>> Error in function (classes, fdef, mtable)  :
>>   unable to find an inherited method for function "Term", for
>> signature "character"
>>
>>> GOTERM$"GO:0006916"
>> GOID: GO:0006916
>> Term: anti-apoptosis
>> Ontology: BP
>> Definition: A process which directly inhibits any of the steps required
>>     for cell death by apoptosis.
>> Synonym: apoptosis inhibitor activity
>>
>> Using GOTERM, I dont know how to capture 'Term'. I cannot use a sapply
>> function over GOTERMS too.
>>
>> -Adrian
>>
>>
>>
>>
>>
>>
>> On Mon, Feb 15, 2010 at 6:53 PM, Heidi Dvinge <heidi at ebi.ac.uk> wrote:
>>> Hello Adrian,
>>>
>>> if you just want the term and nothing else you can say e.g.
>>>
>>>> library(GO.db)
>>> Loading required package: AnnotationDbi
>>> Loading required package: Biobase
>>>
>>> Welcome to Bioconductor
>>>
>>>  Vignettes contain introductory material. To view, type
>>>  'openVignette()'. To cite Bioconductor, see
>>>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>>>
>>> Loading required package: DBI
>>>> Term("GO:0006916")
>>>      GO:0006916
>>> "anti-apoptosis"
>>>
>>>
>>> HTH
>>> \Heidi
>>>> Dear Group,
>>>> Is there any function in GOstats or other packages,  that could give
>>>> term name given GO ID.
>>>>
>>>> I have the result from probeSetSummary. I want to pull the GO term
>>>> name along with GO term ID.
>>>>
>>>> Thanks
>>>> Adrian
>>>>
>>>> _______________________________________________
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>>>>
>>>
>>>
> 
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-- 

Best wishes
      Wolfgang


--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact