[BioC] How to retrieve the GO identifier correctly?

szhan at uoguelph.ca szhan at uoguelph.ca
Tue Oct 12 23:12:08 CEST 2004


Hello, 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
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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