GOTERM by itself
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Auer Michael ▴ 250
@auer-michael-953
Last seen 10.2 years ago
I would like to present the results of GOHyperG in the form of a table with GO ID, Count, Pvalue and GOTERM. The problem lies within the GOTERM ,because the output of the enviroment has changed!!! I am calling GOHyperG with a series of LOCUS IDS, ids1 ids1MF<- GOHyperG(unique(unlist(ids1)),lib="hgu133a",what="MF") Then I am building a matrix with the call. The matrix has the columns GO ID, Counts and pvalues. But I also want the GOTERM. The problem is that there is no function which reports the GOTERM by it self. For example mget("GO:0016407",GOTERM)) $"GO:0016407" GOID = GO:0016407 GO term = acetyltransferase activity Definition for GO term = Catalysis of the transfer of an acetyl group to an acceptor molecule. Ontology = MF But I only want the GOTERM ids1matrMF<-cbind(names(ids1MF$intCounts), as.vector(ids1MF$intCounts), as.vector(ids1MF$pvalues)) dimnames(ids1matrMF)[[2]]<-c(?GO ID?,?Counts?,?pvalues?) How can I retrieve only the GOTERM????? Thanx
GO GO • 1.3k views
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@sean-davis-490
Last seen 3 months ago
United States
Michael, Does the function getGOTerm (from GOstats) do what you want? Sean On Oct 14, 2004, at 6:01 AM, Auer Michael wrote: > I would like to present the results of GOHyperG in the form of a table > with GO ID, Count, Pvalue and GOTERM. The problem lies within the > GOTERM > ,because the output of the enviroment has changed!!! > > > > I am calling GOHyperG with a series of LOCUS IDS, ids1 > > ids1MF<- GOHyperG(unique(unlist(ids1)),lib="hgu133a",what="MF") > > Then I am building a matrix with the call. The matrix has the columns > GO > ID, Counts and pvalues. But I also want the GOTERM. The problem is that > there is no function which reports the GOTERM by it self. > For example mget("GO:0016407",GOTERM)) > > $"GO:0016407" > GOID = GO:0016407 > GO term = acetyltransferase activity > Definition for GO term = Catalysis of the transfer of an acetyl group > to > an acceptor molecule. > Ontology = MF > But I only want the GOTERM > > ids1matrMF<-cbind(names(ids1MF$intCounts), as.vector(ids1MF$intCounts), > as.vector(ids1MF$pvalues)) > dimnames(ids1matrMF)[[2]]<-c(?GO ID?,?Counts?,?pvalues?) > > > > How can I retrieve only the GOTERM????? > > Thanx > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
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SAURIN ★ 1.1k
@saurin-799
Last seen 10.2 years ago
Hi Auer, I would like to do similar thing with GOTERM as you are doing at some extent but I would like to build table like : (I am using Affy chips here) GOTERM ,count of ProbeIDS associated with them , ProbeIDS itself , SYMBOLS of probe ids any idea on this ? Thanks Saurin --- Auer Michael <michael.auer@meduniwien.ac.at> wrote: > I would like to present the results of GOHyperG in > the form of a table > with GO ID, Count, Pvalue and GOTERM. The problem > lies within the GOTERM > ,because the output of the enviroment has changed!!! > > > > I am calling GOHyperG with a series of LOCUS IDS, > ids1 > > ids1MF<- > GOHyperG(unique(unlist(ids1)),lib="hgu133a",what="MF") > > Then I am building a matrix with the call. The > matrix has the columns GO > ID, Counts and pvalues. But I also want the GOTERM. > The problem is that > there is no function which reports the GOTERM by it > self. > For example mget("GO:0016407",GOTERM)) > > $"GO:0016407" > GOID = GO:0016407 > GO term = acetyltransferase activity > Definition for GO term = Catalysis of the transfer > of an acetyl group to > an acceptor molecule. > Ontology = MF > But I only want the GOTERM > > ids1matrMF<-cbind(names(ids1MF$intCounts), > as.vector(ids1MF$intCounts), > as.vector(ids1MF$pvalues)) > dimnames(ids1matrMF)[[2]]<-c(“GO > ID”,”Counts”,”pvalues”) > > > > How can I retrieve only the GOTERM????? > > Thanx > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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On Oct 14, 2004, at 10:21 AM, Saurin Jani wrote: > Hi Auer, > > I would like to do similar thing with GOTERM as you > are doing at some extent but I would like to build > table like : (I am using Affy chips here) > > GOTERM ,count of ProbeIDS associated with them , > ProbeIDS itself , SYMBOLS of probe ids > > any idea on this ? > > Thanks > Saurin Saurin, You can get the probeids associated with a GO term from the GO2PROBES or GO2ALLPROBES environments using lookUp. You can get the symbols of those probes using getSYMBOL. A judicious use of unlist and paste, combined in a final data.frame should do the trick. Sean
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Hi Sean, I got it upto: myLL <- getLL(myDEGenes,"moe430a"); myUNQLL <- as.character(na.omit(unique(unlist(myLL)))); myGOHyp <- GOHyperG(myUNQLL); myGOCC <- GOHyperG(myUNQLL, lib="moe430a", what="CC"); DECCnodes = names(myGOCC$intCounts); CCTERMS <- getGOTerm(DECCnodes); DECCnodes2affy = lookUp(DECCnodes,GO2ALLPROBES); unlist and paste is not working on DECCnodes2affy object as it has: $"GO:0005663" IEA IEA IEA ISS ISS "1418342_at" "1449050_at" "1451920_a_at" "1417503_at" "1423700_at" ISS IEA ISS "1432538_a_at" "1452917_at" "1424321_at now , how can I count each probe ids under GOID in List object. Could you please help me ? Thank you, Saurin --- Sean Davis <sdavis2@mail.nih.gov> wrote: > > On Oct 14, 2004, at 10:21 AM, Saurin Jani wrote: > > > Hi Auer, > > > > I would like to do similar thing with GOTERM as > you > > are doing at some extent but I would like to build > > table like : (I am using Affy chips here) > > > > GOTERM ,count of ProbeIDS associated with them , > > ProbeIDS itself , SYMBOLS of probe ids > > > > any idea on this ? > > > > Thanks > > Saurin > > Saurin, > > You can get the probeids associated with a GO term > from the GO2PROBES > or GO2ALLPROBES environments using lookUp. You can > get the symbols of > those probes using getSYMBOL. A judicious use of > unlist and paste, > combined in a final data.frame should do the trick. > > Sean > >
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Hi, What is difference between GO2ALLPROBES and GO2PROBE? unique(lookUp(DECCnodes[[1]],"moe430a","GO2PROBE")) I get : 76 probes unique(lookUp(DECCnodes[[1]],"moe430a","GO2ALLPROBES")) I get : 281 probes Thanks, Saurin
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Saurin, GO2ALLPROBES maps all probes at a given GO and all probes assigned to its descendents to the GO term in question. GO2PROBES maps only to the GO term in question. Sean On Oct 14, 2004, at 12:20 PM, Saurin Jani wrote: > Hi, > > What is difference between GO2ALLPROBES and GO2PROBE? > > unique(lookUp(DECCnodes[[1]],"moe430a","GO2PROBE")) > I get : 76 probes > > unique(lookUp(DECCnodes[[1]],"moe430a","GO2ALLPROBES")) > I get : 281 probes > > > Thanks, > Saurin > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
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