[BioC] GOTERM

[Robert Gentleman]

First, your R, and hence your Bioconductor packages are a year out of 
date, so you should update them.

Mete Civelek wrote:
> Hi All,
> 
> I have a simple problem that I can't seem to solve. I am using R 2.4.0 on 
> windows. I am trying to get the GO Terms of a list of GO IDs using the 
> following code. The list of GOIDs is in a file labelled SDGO.txt, which is 
> a single column text file with no header.
> 
>  >library(GO)
> 
>  >SDGO<-read.table("SDGO.txt", header=F)
> 
>  >summary(SDGO)
>            V1
>   GO:0000075:  1
>   GO:0000375:  1
>   GO:0000377:  1
>   GO:0000398:  1
>   GO:0001503:  1
>   GO:0001505:  1
>   (Other)   :134
> 
>  >apply(SDGO, 1, GOTERM)
> Error in get(x, envir, mode, inherits) : variable "GOTERM" of mode 
> "function" was not found

  why do you think that is what you should do?

  something more like
   mget(SDGO[,1], GOTERM)

  will be more appropriate

  or sapply(SDGO[,1], getGOTerm)
  would be another alternative


> 
> I am sure I am way off in this code since I am a beginner of R and 
> Bioconductor but I will appreciate any help?

> 
> Best,
> 
> Mete
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org