[BioC] GO's to gene's

[Loren Engrav]

Thank you both
Given my skills, it might be easier/quicker to do it "manually" with Amigo
But I am trying both methods

For the second method I get

> 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
> terms <- Term(GOTERM)
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "Term", for signature
"GOTermsAnnDbBimap"

> sessionInfo()
R version 2.9.2 Patched (2009-09-05 r49613)
i386-apple-darwin9.8.0

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

> From: Martin Morgan <mtmorgan at fhcrc.org>
> Date: Sun, 28 Feb 2010 18:42:33 -0800
> To: Vincent Carey <stvjc at channing.harvard.edu>
> Cc: Loren Engrav <engrav at u.washington.edu>, "bioconductor at stat.math.ethz.ch"
> <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] GO's to gene's
> 
> On 02/28/2010 06:14 PM, Vincent Carey wrote:
>> Perhaps there is a package with such functionality.  However, with the
>> GO.db package in place, you need to do a little
>> programming, perhaps along the lines of
>> 
>> querGO = function(str, attr = "definition", ont = "MF") {
>>   require(GO.db, quietly = TRUE)
>>   gc = GO_dbconn()
>>   quer.1 = paste("select go_id, term from go_term where",
>>   attr, "like('%")
>>   quer.2 = "%') and ontology = '"
>>   quer.3 = "'"
>>   quer = paste(quer.1, str, quer.2, ont, quer.3, collapse = "",
>>   sep = "")
>>   dbGetQuery(gc, quer)
>> }
>> 
>> whereby
>> 
>>> querGO("collagen", "term")
>>        go_id                                                           term
>> 1 GO:0004656                     procollagen-proline 4-dioxygenase activity
>> 2 GO:0005518                                               collagen binding
>> 3 GO:0008475                      procollagen-lysine 5-dioxygenase activity
>> 4 GO:0019797                     procollagen-proline 3-dioxygenase activity
>> 5 GO:0019798                       procollagen-proline dioxygenase activity
>> 6 GO:0033823                       procollagen glucosyltransferase activity
>> 7 GO:0042329 structural constituent of collagen and cuticulin-based cuticle
>> 8 GO:0050211                     procollagen galactosyltransferase activity
>> 9 GO:0070052                                             collagen V binding
>>> 
> 
> Also
> 
>   library(GO.db)
>   terms <- Term(GOTERM)  # or maybe Definition(GOTERM) ?
>   ontologies <- Ontology(GOTERM)
>   collagen <- terms[grepl("collagen", terms) & ("MF" == ontologies)]
> 
> and the next step,
> 
>   library(org.Hs.eg.db)
>   egids <- mget(names(collagen), org.Hs.egGO2EG, ifnotfound=NA)
>   egids <- egids[!is.na(egids)]
> 
> 
>> 
>> On Sun, Feb 28, 2010 at 8:56 PM, Loren Engrav <engrav at u.washington.edu>
>> wrote:
>>> Is there a BioC package that will find all the GO terms containing some
>>> word, like perhaps ³collagen²
>>> And then find all the genes contained within those found terms
>>> 
>>> I scanned
>>> GoProfiles
>>> GOSemSim
>>> GOstats
>>> GoTools and
>>> TopGO
>>> 
>>> And could not determine that any would do that.
>>> 
>>> Thank you.
>>> 
>>> 
>>> 
>>> 
>>>        [[alternative HTML version deleted]]
>>> 
>>> 
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>> 
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> 
> 
> -- 
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
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> 
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