[R] Why I can't retrieve GO identifier correctly?

[Uwe Ligges]

szhan at uoguelph.ca wrote:
> Hello, R experts,
> I tried to retrieve all biological process GO terms at level 3 starting
> "biological process" as level 1 using the code as bellows:
> 
> 1 library(GO)
> 2 library(GOstats)
> 3 level2<-getGOChildren("GO:0008150")$"GO:0008150"$Children
> 4 for ( i in 1:length(level2)) {
> 5    level3 <- getGOChildren(level2[i])$level2[i]$Children

If you want to index by an object that contains a character (or string), 
you have to use "[[]]" rather than "$".
The question is completely independent of GO, so don't confuse potential 
responders who expect you to send messages re. Bioconductor packages to 
the corresponding list.

Uwe Ligges


> 6    for ( j in 1:length(level3)){
> 7       level3term <- getGOTerm(as.character(level3[j]))$BP$level3[j]
> 8       level3term
> 9    }
> 10 }
> What is the difference between line 3 and line5? In the line 3 I retrieved the
> GO identifiers at level 2 successfullly but in the line 5 I got nothing. How to
> correct the line 5 to retrieve the GO terms at level 3 correctly?
> Thank you in advance!
> Josh
> 
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