"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > Consider the following code: > > library(hgu133plus2) > library(GOstats) > library(Rgraphviz) > lls <- unlist(as.list(hgu133plus2ENTREZID))[1:500] > lls <- lls[!is.na(lls)] > univ <- unlist(as.list(hgu133plus2ENTREZID)) > univ <- univ[!is.na(univ)] > params <- new("GOHyperGParams", geneIds=lls, universeGeneIds=univ, > ontology="BP", annotation="hgu133plus2", conditional=TRUE) > hypt <- hyperGTest(params) > grph1 <- getGoGraph(params, summary(hypt)[1:3,1]) > plot(grph1) > grph2 <- GOGraph(summary(hypt)[1:3,1], GOBPPARENTS) > plot(grph2) > > Is the intent that the two graphs should be identical? My reading of > the help page leads me to believe so. I goofed this one up. getGoGraph is used internally to generate the graph used in the computation of the hyperG result. For this purpose, it is more convenient to have the graph with edges pointing to _more_ specific nodes (children) instead of the standard tree view which goes the other way. The method should never have been exported in the first place. Even if I change it to use GOXXPARENTS, all it does is pull out the ontology slot and call GOGraph. It hardly seems worth having, IMO. Thanks for bringing this to my attention. My plan for getGoGraph is: i) make it behave like GOGraph using GOXXPARENTS ii) deprecate it and make it go away asap. I'd rather focus on some useful graph generating methods for the result object. Best Wishes, + seth