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

On Tue, Oct 12, 2004 at 05:12:08PM -0400, szhan@uoguelph.ca wrote: > 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: The difference is that the $ operator does not evaluate its arguments, so it does not do what you think it does in your line 5. Use the [[ ]], version, which does evaluate its argument. Robert ps it is considered to be bad style to post the same request to more than one help list, and it is not helpful to put in line numbers as that makes cut and paste a pain. > > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+