Hi, Alan, I cc'd your question to the list, and please see my answer below: ALAN SMITH wrote: > Hi Nianhua, > Sorry to bother you again. Your advice helped me get through my > problems. I have now run into another problem that is a fairly > serious problem with get.pathways.by.compounds in KEGGSOAP. The > get.pathways.by.compounds only works with your example data. Change > it and it does not work. > > pathways <- try(get.pathways.by.compounds(c("cpd:C00033", > "cpd:C00158"))) #example# > pathways > [1] "path:map00020" "path:map00720" > #It is truncating the pathways only showing the first one in the list# > bget("LIGAND:C00033") > bget("LIGAND:C00158") > No, it doesn't. "get.pathways.by.compounds(c("cpd:C00033", "cpd:C00158"))" returns the pathways that contain BOTH compounds. Try: get.pathways.by.compounds(c("cpd:C00033", "cpd:C00033")) [1] "path:map00010" "path:map00020" "path:map00430" "path:map00440" [5] "path:map00450" "path:map00534" "path:map00620" "path:map00622" [9] "path:map00660" "path:map00720" "path:map00920" get.pathways.by.compounds(c("cpd:C00158", "cpd:C00158")) [1] "path:map00020" "path:map00251" "path:map00252" "path:map00630" [5] "path:map00720" Notice that you always have to give more than one compounds. If there is only one compound, please repeat it (sorry). This is because of a problem in the function. I will try but probably can't fix it quickly. > > The get.pathways.by.compounds only works with your example when I try > this cpd > bget("LIGAND:C00328") > I should recover PATH: map00380 > > pathways <- try(get.pathways.by.compounds(c("cpd:C00033", "cpd:C00328"))) > pathways > #character(0) #does not work# > pathways <- try(get.pathways.by.compounds("cpd:C00328")) > pathways > #character(0) #does not work# Try: get.pathways.by.compounds(c("cpd:C00328", "cpd:C00328")) get.pathways.by.compounds(c("cpd:C00033", "cpd:C00033")) Actually get.pathways.by.compounds(c("cpd:C00033", "cpd:C00328")) should return character(0). I tried it via a java client. > > I have tried many other permutations cpds and none seem to work except > the example Sorry for the inconvenience. Hope it works fine from now on... > > Is there anything you can do to fix this problem? Should I contact > the people at KEGG and explain the problem? The main reason I started > using KEGGSOAP was to get to pathways from neutral masses because the > important biological interpretation of the data is in the pathways. > > Thanks, > Alan Smith best nianhua