search for: goterm

Hi All, I wonder if there should be one character for quote= in read.table, i.e., > args(read.table) function (file, header = FALSE, sep = "", quote = "\"'", dec = ".", ... I have a file containing the following lines, 08248-GOTERM 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process 08279-GOTERM 3'-phosphoadenosine 5'-phosphosulfate binding 08494-GOTERM 'de novo' posttranslational protein folding 08712-GOTERM ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity 08759-GOTE...

...here should be one character for quote= in read.table, i.e., > > >> args(read.table) > function (file, header = FALSE, sep = "", quote = "\"'", dec = ".", > ... > > I have a file containing the following lines, > > > 08248-GOTERM 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process > 08279-GOTERM 3'-phosphoadenosine 5'-phosphosulfate binding > 08494-GOTERM 'de novo' posttranslational protein folding > 08712-GOTERM ATP-dependent polyribonucleotide 5'-hydroxyl-kinase acti...

...ar colleagues, I've just come across a problem with the following command which is a part of the "metaOverview.R" code file provided as an monography- accompanying file at http://www.bioconductor.org/docs/mogr/metadata: ################################## R> hasChr <- eapply(GOTERM, function(x) + x[grep("chromosome", Term(x))]) Error in x[grep("chromosome", Term(x))] : object is not subsettable ################################## I have run the command in the (PPC) Mac OS X R 2.4.1 and (AMD Ubuntu) Linux R 2.4.0 with the same result so it s...

I am running R 2.0.0, GOstats 1.1.1 and GO 1.7.0, and when I use the function GOHyperG, I have the following error: w1<-as.list(hgu95av2LOCUSID) w2<-unique(unlist(w1)) set.seed(123) myLL<-sample(w2,100) xx <- GOHyperG(myLL) Error in mget(x, env = GOTERM, ifnotfound = NA) : recursive default argument reference In fact first I tried this function with my locusId ' list (with affymetrix hgu133plus2), but I had the same error... Any help is appreciated Regards, Sabrina Sabrina Carpentier Service Bioinformatique Institut Curie - Bat. Trouil...

...text html latex example GOMFCHILDREN text html latex example GOMFOFFSPRING text html latex example GOMFPARENTS text html latex example GOQC text html latex GOTERM text html latex example But I never get the "* DONE (GO)" that I'm expecting. Instead, all of the memory on the machine allocates (512MB), it starts to swap out, and never completes. When I look at the output from ps, I see: 8290 pts/5 S+ 0...

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow