Dear all, I am using the following code below in order to retrieve the gene annotations in Gviz package : please could advise on what shall I modify in order to display the HUGO gene symbol on each gene ? thanks ! library("GenomicFeatures") hg18db <- makeTranscriptDbFromUCSC(genome = "hg18",tablename = "knownGene") saveDb(hg18db, file="hg18db_knownGene.sqlite") txdb <-loadDb("hg18db_knownGene.sqlite") txTr <- GeneRegionTrack(txdb,genome="hg18",chromosome="chr9",showId=TRUE,geneS ymbol=TRUE,name="UCSC") plotTracks(txTr,from=start,to=end) -- bogdan ------------------ [[alternative HTML version deleted]]

Dear all, I am using the following code below in order to retrieve the gene annotations in Gviz package : please could advise on what shall I modify in order to display the HUGO gene symbol on each gene ? thanks ! library("GenomicFeatures") hg18db <- makeTranscriptDbFromUCSC(genome = "hg18",tablename = "knownGene") saveDb(hg18db, file="hg18db_knownGene.sqlite") txdb <-loadDb("hg18db_knownGene.sqlite") txTr <- GeneRegionTrack(txdb,genome="hg18",chromosome="chr9",showId=TRUE,geneS ymbol=TRUE,name="UCSC") plotTracks(txTr,from=start,to=end) -- bogdan ------------------ [[alternative HTML version deleted]]

Thanks, Tim ...will do it accordingly. On Mon, Feb 11, 2013 at 3:49 PM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > So the problem (at least as regards my initial code snippet) is that there > is no mapping in the Homo.sapiens OrganismDb for either uc002yjx.1 > or uc010gkz.1 and thus no symbol (since symbol-less features are dropped). > That's sort of odd since, it seems, these are NRIP1 isoforms. > > I noticed that p15 and p16 transcripts appeared to be missing when I > looked at chr9 earlier. This might be an issue where mappings are missing > from Homo.sapiens / org.Hs.eg.db, in which case a posting to the list would > be good. > > Meanwhile, if you want to keep the UCSC names of the genes for which there > is not a Hugo mapping in the symbol table, the following replacement for > subsetting txtr should do it (I tested this): > > ## don't subset txtr. instead, > symbol(txtr)[ hasHugoSymbol ] <- symbolMappings$SYMBOL[hasHugoSymbol] > > Then proceed as before. I get the attached output from running > > plotTracks(txtr,from=start,to=end) > > since the NRIP1 isoforms, not being mapped to Hugo (?!), stay UCSC IDs. > > Do you mind if I cc: the list on this? And/or bring it up with Marc/Herve? > > --t > > > > On Mon, Feb 11, 2013 at 3:19 PM, Bogdan Tanasa <tanasa@gmail.com> wrote: > >> Hi Tim, >> >> I followed your code, in the following way (please see below); >> plotTracks(txtr) works; however, when I try to plot specific regions >> ( eg plotTracks(txtr,chr="chr21", start=15245000,end=15520000) ) it does >> not show the correct region : I suspect it may be an issue in my code, but >> not very sure where ... if you have 2-3 minutes, would appreciate your >> help. thanks ! >> >> library(Homo.sapiens) >> library("ggplot2") >> library(Gviz) >> library("GenomicFeatures") >> library("ggplot2") >> library("rtracklayer") >> library("TxDb.Hsapiens.UCSC.hg18.knownGene") >> >> chr<-"chr21" >> start<-15245000 >> end <-15520000 >> >> hg18db <- makeTranscriptDbFromUCSC(genome = "hg18",tablename = >> "knownGene") >> saveDb(hg18db, file="hg18db_knownGene.sqlite") >> txdb <-loadDb("hg18db_knownGene.sqlite") >> txtr <- >> GeneRegionTrack(txdb,genome="hg18",chromosome="chr21",showId=TRUE,g eneSymbol=TRUE,name="UCSC") >> plotTracks(txtr,from=start,to=end) >> >> >> >> symbolMappings <- select(Homo.sapiens, >> cols=c('UCSCKG','ENTREZID','SYMBOL'), >> keys=symbol(txtr), keytype='UCSCKG') >> symbolMappings <- symbolMappings[match(symbol(txtr), >> symbolMappings$UCSCKG),] >> >> hasHugoSymbol <- !is.na(symbolMappings$SYMBOL) >> >> txtr <- txtr[ hasHugoSymbol ] >> symbol(txtr) <- symbolMappings$SYMBOL[ hasHugoSymbol ] >> >> plotTracks(txtr) >> plotTracks(txtr,from=start,to=end) >> >> >> >> On Mon, Feb 11, 2013 at 11:39 AM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: >> >>> Oops, critical step omitted. See below. >>> >>> ## see ?select for more on the following >>> ## >>> library(Homo.sapiens) >>> symbolMappings <- select(Homo.sapiens, >>> >>> cols=c('UCSCKG','ENTREZID','SYMBOL'), >>> keys=symbol(txtr), >>> keytype='UCSCKG') >>> >>> ## "pork out" the mappings table so that duplicates expand >>> ## >>> symbolMappings <- symbolMappings[match(symbol(txtr), >>> >>> symbolMappings$UCSCKG),] >>> >>> ## if NAs could be accepted as keys, this next step might be unnecessary >>> ## >>> hasHugoSymbol <- !is.na(symbolMappings$SYMBOL) >>> >>> ## however, it seems that not all UCSC known genes have a Hugo symbol? >>> ## >>> txtr <- txtr[ hasHugoSymbol ] >>> symbol(txtr) <- symbolMappings$SYMBOL[ hasHugoSymbol ] >>> plotTracks(txtr) >>> >>> >>> The above (minus comments) is what I used to generate a test result. >>> >>> >>> >>> >>> On Mon, Feb 11, 2013 at 11:34 AM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: >>> >>>> Well, here's one approach. I'll start from the constructed 'txtr' >>>> track. >>>> >>>> ## see ?select for more on the following >>>> ## >>>> library(Homo.sapiens) >>>> symbolMappings <- select(Homo.sapiens, >>>> >>>> cols=c('UCSCKG','ENTREZID','SYMBOL'), >>>> keys=symbol(txtr), >>>> keytype='UCSCKG') >>>> >>>> ## "pork out" the mappings table so that duplicates expand >>>> ## >>>> symbolMappings <- symbolMappings[match(symbol(txtr), >>>> >>>> symbolMappings$UCSCKG),] >>>> >>>> ## if NAs can be accepted as keys, this next step might be unnecessary >>>> ## however, it seems that not all UCSC known genes have a Hugo symbol? >>>> ## >>>> txtr <- txtr[ hasHugoSymbol ] >>>> symbol(txtr) <- symbolMappings$SYMBOL[ hasHugoSymbol ] >>>> plotTracks(txtr) >>>> >>>> That works. >>>> >>>> >>>> >>>> >>>> On Mon, Feb 11, 2013 at 6:03 AM, Hahne, Florian < >>>> florian.hahne@novartis.com> wrote: >>>> >>>>> Well, the main culprit here is really the TranscriptDB package. It does >>>>> not seem to deal at all with gene symbols, so there is no way for Gviz >>>>> to >>>>> automatically fetch those. If you come up with a way to match the UCSC >>>>> gene identifiers back to gene symbols you could stick those into the >>>>> GeneRegionTrack using the 'symbol' replacement method. E.g., >>>>> symbol(foo) <- mappingTable[match(transcript(foo), >>>>> mappingTable$UCSCId),]) >>>>> I am not sure how this mapping is supposed to be done in the >>>>> Bioconductor >>>>> world these days. You may be able to find a way using one of the org.db >>>>> packages. Or maybe you will have to download a mapping table directly >>>>> from >>>>> the UCSC table browser. >>>>> With the next release of Bioconductor (or already now if you are >>>>> working >>>>> with the devel branch), Gviz supports building tracks from a whole >>>>> range >>>>> of standard annotation files. You could then export the whole >>>>> known.gene >>>>> table from UCSC as a GTF file and import in again as a GeneRegionTrack >>>>> object. Alternatively you may want to look into the >>>>> BiomartGeneRegionTrack >>>>> class which will fetch the gene models from Ensembl, but this includes >>>>> the >>>>> HUGO gene symbols. >>>>> Florian >>>>> >>>>> >>>>> -- >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On 2/7/13 10:51 AM, "Bogdan Tanasa" <tanasa@gmail.com> wrote: >>>>> >>>>> >Dear all, >>>>> > >>>>> >I am using the following code below in order to retrieve the gene >>>>> >annotations in Gviz package : >>>>> >please could advise on what shall I modify in order to display the >>>>> HUGO >>>>> >gene symbol on each gene ? thanks ! >>>>> > >>>>> >library("GenomicFeatures") >>>>> >hg18db <- makeTranscriptDbFromUCSC(genome = "hg18",tablename = >>>>> >"knownGene") >>>>> >saveDb(hg18db, file="hg18db_knownGene.sqlite") >>>>> >txdb <-loadDb("hg18db_knownGene.sqlite") >>>>> >txTr <- >>>>> >>>>> >GeneRegionTrack(txdb,genome="hg18",chromosome="chr9",showId=TRU E,geneSymbo >>>>> >l=TRUE,name="UCSC") >>>>> >plotTracks(txTr,from=start,to=end) >>>>> > >>>>> >-- bogdan >>>>> >------------------ >>>>> > >>>>> > [[alternative HTML version deleted]] >>>>> > >>>>> >_______________________________________________ >>>>> >Bioconductor mailing list >>>>> >Bioconductor@r-project.org >>>>> >https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> >Search the archives: >>>>> >http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>> >>>> >>>> >>>> -- >>>> *A model is a lie that helps you see the truth.* >>>> * >>>> * >>>> Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> >>>> >>> >>> >>> >>> -- >>> *A model is a lie that helps you see the truth.* >>> * >>> * >>> Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> >>> >> >> > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > [[alternative HTML version deleted]]