Hello everyone, I wish to filter a list of Gene Ontology terms for the tip terms (most informative GO level) i.e. removing all GO terms which have more general ancestors in the GO hierarchy, also contained in this list. In the graph view this would mean, that after having applied the filter, there should be no GO terms in the graph which have more informative children and successors. I had a look at the different packages dealing with the GO in bioconductor but haven?t found a suitable one so far. Is there by chance anybody, who knows a package in bioconductor, which can be used to tackle this problem? Thanks a lot for your time, Aaron - Aaron Weimann BSc Bioinformatics and Genomics Department Centro de Investigaci?n Pr?ncipe Felipe Avda. Autopista del Saler, 16-3 (junto Oceanogr?fico) 46012 VALENCIA (Spain) Tel: +34 96 328 96 80 Ext. 1011 Fax: +34 96 328 97 01

Hi Aaron, GO.db package has mappings that should be helpful here. There are mappings in there such as GOBPOFFSPRING that can tell you if a particular BP term has any terms that are more terminal than it. There are also mappings for MF and CC in there. so for example, get("GO:0048477", GOBPOFFSPRING) will give you a whole bunch of terms (because is it not a terminal term), but get("GO:0090029", GOBPOFFSPRING) Will get you an NA, because there are no terms that are more terminal than "GO:0090029". Therefore, it is the most informative term you can use in that part of the DAG. Also, you can use the Ontology() method to make sure you use the correct mapping for your terms. For example Ontology("GO:0090029") Will tell you that the term "GO:0090029" is part of the "BP" ontology (not the MF or CC branches), which you will need to be sure of before concluding that an NA from, "get("GO:0090029", GO*BP*OFFSPRING)" really means that your term is terminal. Hope this helps, Marc On 10/13/2010 07:32 AM, Aaron Weimann wrote: > Hello everyone, > > I wish to filter a list of Gene Ontology terms for the tip terms (most > informative GO level) i.e. removing all GO terms which have more > general ancestors in the GO hierarchy, also contained in this list. In > the graph view this would mean, that after having applied the filter, > there should be no GO terms in the graph which have more informative > children and successors. > I had a look at the different packages dealing with the GO in > bioconductor but haven´t found a suitable one so far. Is there by > chance anybody, who knows a package in bioconductor, which can be > used to tackle this problem? > > Thanks a lot for your time, > > Aaron > > - > Aaron Weimann BSc > Bioinformatics and Genomics Department > > Centro de Investigación Príncipe Felipe > Avda. Autopista del Saler, 16-3 (junto Oceanográfico) > 46012 VALENCIA (Spain) > Tel: +34 96 328 96 80 Ext. 1011 > Fax: +34 96 328 97 01 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]