Hi, I build an annotation package for a mouse IPI database using "AnnotationDbi" (IPI.MOUSE.3.37.20080509.db) and am now putting it to use. I have a bunch of IPI-ID clusters ("SubjectiveClusters") each of which I want to check for GO terms significantly enriched over the combined set. I attached what I do, but was wondering whether ther's ways to do this without having to explicitly/manually go via ENTREZ IDs. The annotation package contains all information necessary already, no? Is there anything more recent than "GOstats" to look at this? Thanks, Joh library(IPI.MOUSE.3.37.20080509.db) library("GOstats") # Extract all IPI to ENTREZID pairs ENTREZIDs <- IPI.MOUSE.3.37.20080509ENTREZID # Combine all present IPI IDs to the Universe Universe <- unlist(SubjectiveClusters,use.names=FALSE) # Purge IPIs not mapping to ENTREZ Universe <- Universe[Universe %in% mappedkeys(ENTREZIDs)] # Map universe to ENTREZ IDs Universe <- unique(unlist(as.list(ENTREZIDs[Universe]),use.names=FALSE)) SubjectiveClustersHGT <- vector("list",0) for(name in names(SubjectiveClusters)){ Temp.Cluster <- SubjectiveClusters[[name]] Temp.Cluster <- Temp.Cluster[Temp.Cluster %in% mappedkeys(ENTREZIDs)] Temp.Cluster <- unlist(as.list(ENTREZIDs[Temp.Cluster]),use.names=FALSE) params <- new( "GOHyperGParams", geneIds = Temp.Cluster, universeGeneIds = Universe, annotation = "IPI.MOUSE.3.37.20080509.db", ontology = "BP", pvalueCutoff = 0.01, conditional = TRUE, testDirection = "over" ) cat("HyperGTest for cluster ",name,".\n",sep="") SubjectiveClustersHGT[[name]] <- hyperGTest(params) }

Hi Johannes, Johannes Graumann wrote: > Hi, > > I build an annotation package for a mouse IPI database using "AnnotationDbi" > (IPI.MOUSE.3.37.20080509.db) and am now putting it to use. > I have a bunch of IPI-ID clusters ("SubjectiveClusters") each of which I > want to check for GO terms significantly enriched over the combined set. I > attached what I do, but was wondering whether ther's ways to do this > without having to explicitly/manually go via ENTREZ IDs. The annotation > package contains all information necessary already, no? Is there anything > more recent than "GOstats" to look at this? Did you have a look at the vignette? It does seem to explain how to do this (and there are examples, such as the YEAST package which do not use EntrezGene IDs). What is essential is that the geneIds and universeGeneIds match and that this is the same type of identifier that you made the primary key when you made your annotation package (so that given one of these you can find all relevant GO terms, but that is an AnnotationDbi question). > > Thanks, Joh > > library(IPI.MOUSE.3.37.20080509.db) > library("GOstats") > # Extract all IPI to ENTREZID pairs > ENTREZIDs <- IPI.MOUSE.3.37.20080509ENTREZID > # Combine all present IPI IDs to the Universe > Universe <- unlist(SubjectiveClusters,use.names=FALSE) > # Purge IPIs not mapping to ENTREZ > Universe <- Universe[Universe %in% mappedkeys(ENTREZIDs)] > # Map universe to ENTREZ IDs > Universe <- unique(unlist(as.list(ENTREZIDs[Universe]),use.names=FALSE)) > SubjectiveClustersHGT <- vector("list",0) > for(name in names(SubjectiveClusters)){ > Temp.Cluster <- SubjectiveClusters[[name]] > Temp.Cluster <- Temp.Cluster[Temp.Cluster %in% mappedkeys(ENTREZIDs)] > Temp.Cluster <- unlist(as.list(ENTREZIDs[Temp.Cluster]),use.names=FALSE) > params <- new( > "GOHyperGParams", > geneIds = Temp.Cluster, > universeGeneIds = Universe, > annotation = "IPI.MOUSE.3.37.20080509.db", > ontology = "BP", > pvalueCutoff = 0.01, > conditional = TRUE, > testDirection = "over" > ) > cat("HyperGTest for cluster ",name,".\n",sep="") > SubjectiveClustersHGT[[name]] <- hyperGTest(params) > } > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org