A few more comments on this. Because to answer your questions you can also use some of the nice graph stuff in the project: ## So you can load a few useful libraries library(GO.db) ## for GO library(graph) ## for basic graph containers etc. library(RBGL) ## for algorithms to compute distance etc. ## 1st lets just make the PARENTS object into a nice tabular format with the toTable() method like this: xx = toTable(GOBPPARENTS) ## For now lets assume that we don't care what kind of relationship is represented, and just make that whole table into a graph with all edge weights set = 1. ## The reason I am setting the weights to 1 is so that later on I can more easily compute the distances. gg = ftM2graphNEL(as.matrix(xx[, 1:2]), W=rep(1,dim(xx)[1])) ## 'from / to' columns, with weights 'W' all set to 1 ## And if you want to visualize your graph it you can use Rgraphviz library(Rgraphviz) ## for plotting graph objects ## But lets not draw everything. Instead lets grab a subgraph containing only the nodes that we care about... sg <- subGraph(c(get("GO:0006955", GOBPANCESTOR), "GO:0006955"), gg) ## Then plot it plot(sg) ## And then we can use tools from RBGL to compute distance in terms of the number of edges... dijkstra.sp(sg, "GO:0006955")$distances["GO:0008150"] dijkstra.sp(sg, "GO:0006955")$distances["all"] Hope this helps, Marc On 01/14/2013 11:19 AM, Marc Carlson wrote: > Also I forgot to mention, > > You can get the immediate parent to any term by using the appropriate > PARENTS object. So for example: > > get("GO:0006955", GOBPPARENTS) > > Will tell you that there are TWO immediate parents for this term. > Which is the situation I was describing earlier. > > > Marc > > > On 01/14/2013 11:09 AM, Marc Carlson wrote: >> Hi Nicos, >> >> You could use the GO.db package to get at this. In there you will >> find an object called GOBPANCESTOR which acts like a classic R >> environment object and can be used with the get() method to pull out >> the ancestor terms of a given term all the way back to the root. >> >> So for your example you could have done this: >> >> library(GO.db) >> get("GO:0008150", GOBPANCESTOR) >> >> And you can see that the only ancestor to this term is in fact the >> root node: "all" >> >> >> What about terms further down? Well the same trick works for all the >> terms to get their ancestor terms: >> get("GO:0006955", GOBPANCESTOR) >> >> >> >> So you probably want to do something a bit like this: >> >> length(get("GO:0006955", GOBPANCESTOR)) >> >> And (for example) compare that to: >> >> length(get("GO:0008150", GOBPANCESTOR)) >> >> etc. >> >> >> Of course it's all a little bit more complicated than that because >> the gene ontologies are actually DAGs (so terms can have more than >> one route back to the main node), and so your ancestors list may be >> longer than just the simple path back to the "all" node. And in fact >> in the example I gave above this is true for the further down term >> "GO:0006955", which has two routes back to the main node, and hence >> it's "distance" (as hinted at by length) has been inflated by one in >> this case. >> >> >> Anyhow, I hope this helps, >> >> >> Marc >> >> >> >> >> >> On 01/14/2013 07:47 AM, WoA [guest] wrote: >>> Given some GO BP terms for a gene I wish to find out, which of the >>> terms has more specific meaning. I wish to find out the length of >>> the shortest path between the BP Root term(GO:0008150) and the given >>> term. Is there any suitable way to do that using any R package? >>> >>> Like something equivalent to: >>> my $length = $node->lengthOfShortestPathToRoot; >>> >>> in Perl's "GO-TermFinder" package. >>> >>> Thanks in advance >>> >>> -- output of sessionInfo(): >>> >>>> sessionInfo() >>> R version 2.13.1 (2011-07-08) >>> Platform: i386-pc-mingw32/i386 (32-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_United States.1252 >>> [2] LC_CTYPE=English_United States.1252 >>> [3] LC_MONETARY=English_United States.1252 >>> [4] LC_NUMERIC=C >>> [5] LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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