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

[szhan@uoguelph.ca]

Hello, Uwe and Robert,
Thank you for your help! I fixed the problem as your suggestion. I run into a
new issue: I can't sink the output to a file in the script within loops as
bellows, but I can sink it in the command line( I run R1.9.1 on WinXP).
The scrip:
sink("C:/level3BPterm.txt")
level2<-getGOChildren("GO:0008150")$"GO:0008150"$Children
for ( i in 1:length(level2)) {

    level3 <- c(getGOChildren(level2[i])[[1]]$Children)
    for ( j in 1:length(level3)){

       level3term <- getGOTerm(as.character(level3[j]))$BP

       paste(level3term)

    }
}
sink()

Run in the command line:
> sink("C:/level3BPterm.txt")
>  paste(level3term)
> sink()
So what is wrong with my script?
Thanks again
Josh

Quoting Uwe Ligges <ligges at statistik.uni-dortmund.de>:

> 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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