[BioC] GO terms

[michael watson (IAH-C)]

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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
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>>>
>>
>>
>>
>

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