Hi Adrian the function "Term" is defined in the AnnotationDbi package, which you need to have attached to your search path in order to use it. The following works for me: library("GO.db") Term("GO:0006916") ## "anti-apoptosis" Definition("GO:0006916") ## "A process which directly inhibits any of the steps required for cell ## death by apoptosis." Also see the man page ("? Term") for other useful accessor functions. > sessionInfo() R version 2.11.0 Under development (unstable) (2010-02-15 r51142) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GO.db_2.3.5 RSQLite_0.8-3 DBI_0.2-5 [4] AnnotationDbi_1.9.4 Biobase_2.7.4 fortunes_1.3-7 loaded via a namespace (and not attached): [1] tools_2.11.0 Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact michael watson (IAH-C) scripsit 02/16/2010 10:27 AM: > I have no idea if this helps, but the first thing I do with GO.db is turn it into a data.frame. > I realise this loses the hierarchical structure, but it is invaluable if you want to use functions such as merge(). > > library(GO.db) > xx <- as.list(GOTERM) > foo <- function(x) c(GOID(x), Term(x),Definition(x), Ontology(x)) > gomat <- t(sapply(xx, foo, simplify=TRUE)) > gomat <- as.data.frame(gomat) > colnames(gomat) <- c("ID","Term","Definition","Ontology") > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto :bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Heidi Dvinge > Sent: 16 February 2010 00:15 > To: Adrian Johnson > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] GO terms > > Hello Adrian, > > could you perhaps provide your sessionInfo? When I use the examples > provide on probeSetSummary in GOstats to create an object called ps, I can > then say: > >> ps[1] > $`GO:0043412` > EntrezID ProbeSetID selected > 1 10114 102_at 1 > 2 10114 41501_at 0 > 3 10114 41502_at 0 > 4 10152 1040_s_at 1 > 5 10152 135_g_at 0 > ... > >> names(ps)[1:10] > [1] "GO:0043412" "GO:0006796" "GO:0006468" "GO:0044267" "GO:0044260" > "GO:0042221" "GO:0002520" > [8] "GO:0045321" "GO:0044419" "GO:0030097" >> Term(names(ps)[1:10]) > GO:0043412 > GO:0006796 > "biopolymer modification" "phosphate > metabolic process" > GO:0006468 > GO:0044267 > "protein amino acid phosphorylation" "cellular protein > metabolic process" > GO:0044260 > GO:0042221 > "cellular macromolecule metabolic process" "response to > chemical stimulus" > GO:0002520 > GO:0045321 > "immune system development" > "leukocyte activation" > GO:0044419 > GO:0030097 > "interspecies interaction between organisms" > "hemopoiesis" >> sessionInfo() > R version 2.10.0 (2009-10-26) > i386-apple-darwin8.11.1 > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GO.db_2.3.5 GOstats_2.12.0 graph_1.24.0 > Category_2.12.0 annotate_1.24.0 > [6] hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 DBI_0.2-4 > AnnotationDbi_1.8.0 > [11] affy_1.24.0 Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 genefilter_1.28.0 GSEABase_1.8.0 > preprocessCore_1.8.0 > [5] RBGL_1.22.0 splines_2.10.0 survival_2.35-7 > tools_2.10.0 > [9] XML_2.6-0 xtable_1.5-5 > > > >> Hi Heidi, >> Thanks for quick reply. >> It doesnt work for me. Although GOTERMS$"GO:ID" works. >> >> I have all my GOIDs in a list, I want to get the terms for that IDs in >> character vector. >> >> >>> Term("GO:0006916") >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "Term", for >> signature "character" >> >>> GOTERM$"GO:0006916" >> GOID: GO:0006916 >> Term: anti-apoptosis >> Ontology: BP >> Definition: A process which directly inhibits any of the steps required >> for cell death by apoptosis. >> Synonym: apoptosis inhibitor activity >> >> Using GOTERM, I dont know how to capture 'Term'. I cannot use a sapply >> function over GOTERMS too. >> >> -Adrian >> >> >> >> >> >> >> On Mon, Feb 15, 2010 at 6:53 PM, Heidi Dvinge <heidi at="" ebi.ac.uk=""> wrote: >>> Hello Adrian, >>> >>> if you just want the term and nothing else you can say e.g. >>> >>>> library(GO.db) >>> Loading required package: AnnotationDbi >>> Loading required package: Biobase >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'openVignette()'. To cite Bioconductor, see >>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>> >>> Loading required package: DBI >>>> Term("GO:0006916") >>> GO:0006916 >>> "anti-apoptosis" >>> >>> >>> HTH >>> \Heidi >>>> Dear Group, >>>> Is there any function in GOstats or other packages, that could give >>>> term name given GO ID. >>>> >>>> I have the result from probeSetSummary. I want to pull the GO term >>>> name along with GO term ID. >>>> >>>> Thanks >>>> Adrian >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> > > _______________________________________________ > 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 > > _______________________________________________ > 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 --

Hi Michael another way of doing that is tt = toTable(GOTERM) Best wishes Wolfgang watson (IAH-C) scripsit 02/16/2010 10:27 AM: > I have no idea if this helps, but the first thing I do with GO.db is turn it into a data.frame. > I realise this loses the hierarchical structure, but it is invaluable if you want to use functions such as merge(). > > library(GO.db) > xx <- as.list(GOTERM) > foo <- function(x) c(GOID(x), Term(x),Definition(x), Ontology(x)) > gomat <- t(sapply(xx, foo, simplify=TRUE)) > gomat <- as.data.frame(gomat) > colnames(gomat) <- c("ID","Term","Definition","Ontology") > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto :bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Heidi Dvinge > Sent: 16 February 2010 00:15 > To: Adrian Johnson > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] GO terms > > Hello Adrian, > > could you perhaps provide your sessionInfo? When I use the examples > provide on probeSetSummary in GOstats to create an object called ps, I can > then say: > >> ps[1] > $`GO:0043412` > EntrezID ProbeSetID selected > 1 10114 102_at 1 > 2 10114 41501_at 0 > 3 10114 41502_at 0 > 4 10152 1040_s_at 1 > 5 10152 135_g_at 0 > ... > >> names(ps)[1:10] > [1] "GO:0043412" "GO:0006796" "GO:0006468" "GO:0044267" "GO:0044260" > "GO:0042221" "GO:0002520" > [8] "GO:0045321" "GO:0044419" "GO:0030097" >> Term(names(ps)[1:10]) > GO:0043412 > GO:0006796 > "biopolymer modification" "phosphate > metabolic process" > GO:0006468 > GO:0044267 > "protein amino acid phosphorylation" "cellular protein > metabolic process" > GO:0044260 > GO:0042221 > "cellular macromolecule metabolic process" "response to > chemical stimulus" > GO:0002520 > GO:0045321 > "immune system development" > "leukocyte activation" > GO:0044419 > GO:0030097 > "interspecies interaction between organisms" > "hemopoiesis" >> sessionInfo() > R version 2.10.0 (2009-10-26) > i386-apple-darwin8.11.1 > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GO.db_2.3.5 GOstats_2.12.0 graph_1.24.0 > Category_2.12.0 annotate_1.24.0 > [6] hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 DBI_0.2-4 > AnnotationDbi_1.8.0 > [11] affy_1.24.0 Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 genefilter_1.28.0 GSEABase_1.8.0 > preprocessCore_1.8.0 > [5] RBGL_1.22.0 splines_2.10.0 survival_2.35-7 > tools_2.10.0 > [9] XML_2.6-0 xtable_1.5-5 > > > >> Hi Heidi, >> Thanks for quick reply. >> It doesnt work for me. Although GOTERMS$"GO:ID" works. >> >> I have all my GOIDs in a list, I want to get the terms for that IDs in >> character vector. >> >> >>> Term("GO:0006916") >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "Term", for >> signature "character" >> >>> GOTERM$"GO:0006916" >> GOID: GO:0006916 >> Term: anti-apoptosis >> Ontology: BP >> Definition: A process which directly inhibits any of the steps required >> for cell death by apoptosis. >> Synonym: apoptosis inhibitor activity >> >> Using GOTERM, I dont know how to capture 'Term'. I cannot use a sapply >> function over GOTERMS too. >> >> -Adrian >> >> >> >> >> >> >> On Mon, Feb 15, 2010 at 6:53 PM, Heidi Dvinge <heidi at="" ebi.ac.uk=""> wrote: >>> Hello Adrian, >>> >>> if you just want the term and nothing else you can say e.g. >>> >>>> library(GO.db) >>> Loading required package: AnnotationDbi >>> Loading required package: Biobase >>> >>> Welcome to Bioconductor >>> >>> Vignettes contain introductory material. To view, type >>> 'openVignette()'. To cite Bioconductor, see >>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>> >>> Loading required package: DBI >>>> Term("GO:0006916") >>> GO:0006916 >>> "anti-apoptosis" >>> >>> >>> HTH >>> \Heidi >>>> Dear Group, >>>> Is there any function in GOstats or other packages, that could give >>>> term name given GO ID. >>>> >>>> I have the result from probeSetSummary. I want to pull the GO term >>>> name along with GO term ID. >>>> >>>> Thanks >>>> Adrian >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >>> > > _______________________________________________ > 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 > > _______________________________________________ > 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 -- Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact