[BioC] How to get Gene ontology (GO) terms per probe

Rafi [guest] guest at bioconductor.org
Wed Oct 24 00:59:52 CEST 2012

I am new to R/BioC. I am trying to do GO-based clustering of genes. The input (for the package csbl.go) needs to be gene name and GO terms in each row. Example:

AP4B1 GO:0005215 GO:0005488 GO:0005515 GO:0005625 
BCAS2 GO:0005515 GO:0005634 GO:0005681 GO:0008380 

I tried using annotate in bioconductor:

testid<-c("1367462_at","1380262_at", "1392516_a_at", "1396521_at")
goid1 <- rat2302GO[testid]

But I get only each GO term in seperate row:


probe_id      go_id Evidence Ontology
1  1367462_at GO:0008152      IEA       BP
2  1367462_at GO:0008152      ISO       BP
3  1367462_at GO:0006508      IMP       BP
4  1367462_at GO:0005886      IEA       CC
5  1367462_at GO:0005737      IEA       CC
6  1380262_at GO:0005575       ND       CC
7  1380262_at GO:0005634      IEA       CC
8  1380262_at GO:0005737      IEA       CC
9  1367462_at GO:0005509      IEA       MF
10 1367462_at GO:0005509      TAS       MF

Is there any easier way to get all GO terms per gene/probe?

Any help is greatly appreciated.


 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] csbl.go_1.4.0        RUnit_0.4.26         cluster_1.14.2       GO.db_2.7.1          BiocInstaller_1.4.9 
 [6] annotate_1.34.1      rat2302.db_2.7.1     org.Rn.eg.db_2.7.1   RSQLite_0.11.1       DBI_0.2-5           
[11] AnnotationDbi_1.18.1 Biobase_2.16.0       BiocGenerics_0.2.0  

loaded via a namespace (and not attached):
[1] IRanges_1.14.4 stats4_2.15.0  tools_2.15.0   XML_3.9-4.1    xtable_1.7-0 

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