[BioC] GOHyperG function with ath1121501

[Robert Gentleman]

Hi,
  Not easily. Basically the current mapping is from Entrez Gene IDs to 
GO. So if you have a different system for going to GO categories you 
would need to modify the code accordingly. That is sort of the essential 
piece - how do you go from your IDs to GO categories, after that it is 
just hypergeometric calculations.


  Best wishes,
    Robert


Thomas Girke wrote:
> I have a question regarding GOHyperG function in GOstat. Is it
> possible to use this function with the Arabidopsis ath1121501
> annotation package? The function GOHyperG requires a vector of
> LocusLink identifiers, however LocusLink identifiers don't seem to be 
> available in the latest ath1121501 package since it is based on
> data sources from the Tair project (which is a good choice).
> Is there a way to work around this limitation and use this annotation
> package with GOHyperG?
> 
> I have tried to use alternative loci identifiers, but this resulted
> in the below error message. Here is an example of what I have tried to do:
> 
> 
>>library(GOstats)
>>library(ath1121501)
>>library(GO)
>>zz1<-as.list(ath1121501ACCNUM) # or any other available mapping
>>zz2<-unique(unlist(zz1))[1:100]
>>xx<-GOHyperG(zz2, lib="ath1121501", what="MF")
> 
> 
> Error in get(x, envir, mode, inherits) : variable "ath1121501LOCUSID" of mode "environment" was not found
> Error in as.list(getDataEnv("LOCUSID", lib)) :
> unable to find the argument 'x' in selecting a method for function 'as.list'
> 
> Thanks,
> 
> Thomas
>