[BioC] problem with makeGOGraph function

[James W. MacDonald]

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!
>
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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