Hello, the help information for org.Xx.egGO appears to be incomplete - the help says The Evidence element contains a code indicating what kind of evidence supports the association of the GO identifier to the Entrez Gene id. The evidence codes in use include: IMP: inferred from mutant phenotype IGI: inferred from genetic interaction IPI: inferred from physical interaction ISS: inferred from sequence similarity IDA: inferred from direct assay IEP: inferred from expression pattern IEA: inferred from electronic annotation TAS: traceable author statement NAS: non-traceable author statement ND: no biological data available IC: inferred by curator According to the GO web site at http://www.geneontology.org/GO.evidence.shtml, there are many more codes (22, to be precise). It would be great if the codes could be listed in the help file, or at least if the help explicitly said that this is not the full listing of possible codes and referred the reader the web site for more details. Incidentally, the help for GO[BP,CC,MF]OFFSPRING also contains a typo: it says The format is an R object mapping the GO MF terms to all offspring terms, where an ancestor term is a more specific GO term that is preceded by the given GO term in the DAG (in other words, the children and all their children, etc.). The word "ancestors" should be replaced by "offspring". Thanks, Peter

Thanks for the feedback Peter. I have updated the affected manual page templates so that future manual pages can be a little clearer. Marc On 05/02/2013 08:47 PM, Peter Langfelder wrote: > Hello, > > the help information for org.Xx.egGO appears to be incomplete - the help says > > The Evidence element contains a code indicating what kind of > evidence supports the association of the GO identifier to the > Entrez Gene id. The evidence codes in use include: > > IMP: inferred from mutant phenotype > IGI: inferred from genetic interaction > IPI: inferred from physical interaction > ISS: inferred from sequence similarity > IDA: inferred from direct assay > IEP: inferred from expression pattern > IEA: inferred from electronic annotation > TAS: traceable author statement > NAS: non-traceable author statement > ND: no biological data available > IC: inferred by curator > > According to the GO web site at > http://www.geneontology.org/GO.evidence.shtml, there are many more > codes (22, to be precise). It would be great if the codes could be > listed in the help file, or at least if the help explicitly said that > this is not the full listing of possible codes and referred the reader > the web site for more details. > > Incidentally, the help for GO[BP,CC,MF]OFFSPRING also contains a typo: it says > > The format is an R object mapping the GO MF terms to all offspring > terms, where an ancestor term is a more specific GO term that is > preceded by the given GO term in the DAG (in other words, the > children and all their children, etc.). > > The word "ancestors" should be replaced by "offspring". > > Thanks, > > Peter > > _______________________________________________ > 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