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

[Uwe Ligges]

szhan at uoguelph.ca wrote:

> Hello, Uwe and Robert,

Well, you are sending your message to Uwe and R-help rather than "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)

You need to print() it! But you really want to return() it from a 
function ...

Uwe

>     }
> }
> 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
>>>
>>>______________________________________________
>>>R-help at stat.math.ethz.ch mailing list
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>>>PLEASE do read the posting guide!
>>
>>http://www.R-project.org/posting-guide.html
>>
> 
>