[BioC] RE : problem with makeGOGraph function

[James W. MacDonald]

Hi Samuel,

If you want more help, you will have to supply us with a small, self 
contained example that results in the error you see. When I tested the 
suggested code below, it worked, so you must be doing something different.

Best,

Jim


On 3/30/2014 10:23 AM, Samuel Rochette wrote:
> Dear James,
>
> thank you very much for your help. Although your suggestion makes a lot of sense, it seems that there is still a problem. When I type the command line that you suggested, the following error message appears: "Erreur dans newNodes[[i]] : indice hors limites".
>
> Please let me know if you have any other suggestion.
>
> Best.
>
> Samuel Rochette
>
> ________________________________________
> De : James W. MacDonald [jmacdon at uw.edu]
> Date d'envoi : 27 mars 2014 18:17
> À : Samuel Rochette [guest]
> Cc : bioconductor at r-project.org; Samuel Rochette
> Objet : Re: [BioC] problem with makeGOGraph function
>
> Hi Samuel,
>
>
> On 3/27/2014 2:51 PM, Samuel Rochette [guest] wrote:
>> Hi,
>>
>> I wish to produce a directed acyclic graph of a gene enrichment analysis that I performed using R GOstats package. For this, I wanted to use the makeGOGraph function, but it seems that there is a problem when using the yeast data base package "org.Sc.sgd.db".
>>
>> Here is the command line:
>>
>>> tree <- makeGOGraph(hits.list[[1]]$sys, Ontology="BP", removeRoot=TRUE,chip="org.Sc.sgd.db")
>> where "hits.list[[1]]$sys" is a vector containing yeast genes.
>>
>>    -- output of sessionInfo():
>>
>> Here is the error message:
>>
>> "Erreur dans .get_eg_to_go_fun(mapfun, chip) :
>>     either mapfun or chip must be specified
>> De plus : Message d'avis :
>> objet 'org.Sc.sgdGO2PROBE' introuvable
>> DB-based version of  org.Sc.sgd.db  not found.
>> Reverting to use of environment-based GO"
>>
>> It seems that there is something missing in the org.Sc.sgd.db package but I could not find out what exactly.
> The problem here is that the function is really expecting that you are
> using a chip-level package, rather than an organism level package. So
> there is some functionality under the hood that tries to map chip probe
> IDs to the respective GO IDs. Since you aren't doing that, you have to
> supply a function that will do that for you.
>
> Try this and see if it helps
>
> myFun <- function(x){
> tmp <- mget(x, org.Sc.sgdGO, ifnotfound = NA)
> names(tmp) <- NULL
> unlist(tmp, recursive = FALSE)
> }
>
> tree <- makeGOGraphs(hits.list[[1]]$sys, Ontology = "BP", removeRoot =
> TRUE, mapfun = myFun)
>
> Best,
>
> Jim
>
>
>> Thank you for your help!
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099