Hi everybody, I have a problem working with GO annotations. I would like to group my data according to their GO categories, but only of one level. I have a data.frame (three columns: WT, mutation, mean(WT/mutation) and ca. 3150 rows) row.names mut WT WT_mut 1737_Sepsecs 0.6924728 0.00728067 95.111137 1478_Ube2m 4.6102070 0.11428570 40.339316 2807_Pla2g4c 1.7234250 0.04276977 40.295400 2361_Trmt5 1.0203870 0.03652034 27.940238 I also have the GO categories for each of this rows( the names are MGI symbols from the mouse genome). Unfortunately I have ALL the GO annotations. I would like to filter them according to the GO categories of a specific level(!). It doesn't matter whether 'MF', 'BP' or 'CC' yet. But I couldn't find anywhere a way of extracting just that. I would like to know whether there is a way of extracting GO annotations of a specific level from the GO annotation package. Thanks in advance Assa Yeroslaviz [[alternative HTML version deleted]]

Hi Assa, Did you try to use the Ontology() helper function? Something like this: library(GO.db) Ontology(c("GO:0000003","GO:0000007")) There are a series of helper functions like this for GO terms (Term, Ontology, Definition etc.) You can read more about them in the man pages if you are interested. I really hope this helps. But I am having a little trouble understanding your email. So if I have missed the mark then please give me a few more details about what you have and what you want to do. Marc On 03/17/2011 08:07 AM, Assa Yeroslaviz wrote: > Hi everybody, > > I have a problem working with GO annotations. > I would like to group my data according to their GO categories, but only of > one level. > I have a data.frame (three columns: WT, mutation, mean(WT/mutation) and ca. > 3150 rows) > row.names mut WT WT_mut > 1737_Sepsecs 0.6924728 0.00728067 95.111137 > 1478_Ube2m 4.6102070 0.11428570 40.339316 > 2807_Pla2g4c 1.7234250 0.04276977 40.295400 > 2361_Trmt5 1.0203870 0.03652034 27.940238 > > I also have the GO categories for each of this rows( the names are MGI > symbols from the mouse genome). > > Unfortunately I have ALL the GO annotations. I would like to filter them > according to the GO categories of a specific level(!). It doesn't matter > whether 'MF', 'BP' or 'CC' yet. > But I couldn't find anywhere a way of extracting just that. > > I would like to know whether there is a way of extracting GO annotations of > a specific level from the GO annotation package. > > Thanks in advance > > Assa Yeroslaviz > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor