[EMAIL PROTECTED] 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 <[EMAIL PROTECTED]>:
[EMAIL PROTECTED] 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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