[BioC] GO terms
Wolfgang Huber
whuber at embl.de
Tue Feb 16 17:50:00 CET 2010
Hi Adrian
the function "Term" is defined in the AnnotationDbi package, which you
need to have attached to your search path in order to use it. The
following works for me:
library("GO.db")
Term("GO:0006916")
## "anti-apoptosis"
Definition("GO:0006916")
## "A process which directly inhibits any of the steps required for cell
## death by apoptosis."
Also see the man page ("? Term") for other useful accessor functions.
> sessionInfo()
R version 2.11.0 Under development (unstable) (2010-02-15 r51142)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] GO.db_2.3.5 RSQLite_0.8-3 DBI_0.2-5
[4] AnnotationDbi_1.9.4 Biobase_2.7.4 fortunes_1.3-7
loaded via a namespace (and not attached):
[1] tools_2.11.0
Best wishes
Wolfgang
--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact
michael 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>>>
>>>
>>>
>
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