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Question: Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands
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5.8 years ago by
Guest User12k
Guest User12k wrote:
The first problem I have was with ideoTrack. I am using genome<-'danRer7' and when I perform: > genome<-"danRer7" > myGene<-getGenes(cuff_data,'cdk6') > myChr<-unique(features(myGene)$seqnames) > ideoTrack <- IdeogramTrack(genome = genome, chromosome = myChr) I receive the following error message: Error in normArgTrack(track, trackids) : Unknown track: cytoBandIdeo I don't know how to get around this. I have tried to use chr1 for chromosome and get same error. I have tried to use older versions of the genome as well (i.e. 'danRer6', 'danRer5', etc. and receive the same error). I have tried to use 'Zv9" and I get the error that it is not a valid UCSC genome. I can use the human genome 'hg19' and for some reason I don't understand it actually will pull up the zebrafish 'Zv9' location, but this causes problems downstream with the biomaRt commands. Secondly, I am having problems with the biomaRt command. When I enter the command: >biomTrack<-BiomartGeneRegionTrack(genome=genome,chromosome=as.charact er(myChr),start=myStart,end=myEnd,name="ENSEMBL",showId=T) I receive the following error: Error in .genome2Dataset(genome) : Unable to automatically determine Biomart data set for UCSC genome 'danRer7' The danRer7 is, but it will not automatically fetch the Biomart data set. I have also tried using earlier versions of the zebrafish genome (i.e. danRer6, danRer5, etc.) but I get the same error. Again, I have tried using other names for the genome that may work for the biomaRt, such as 'Zv9' and 'Danio rerio genes (Zv9)', but then it tells me that it is not a valid UCSC genome. Can you help me with this? Any and all help would be very much appreciated. Thanks so much -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] cummeRbund_2.0.0 Gviz_1.2.1 rtracklayer_1.18.2 GenomicRanges_1.10.6 IRanges_1.16.4 fastcluster_1.1.7 [7] reshape2_1.2.2 ggplot2_0.9.3 RSQLite_0.11.2 DBI_0.2-5 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.20.3 Biobase_2.18.0 biomaRt_2.14.0 Biostrings_2.26.2 biovizBase_1.6.2 [6] bitops_1.0-4.2 BSgenome_1.26.1 cluster_1.14.3 colorspace_1.2-0 dichromat_1.2-4 [11] digest_0.6.0 GenomicFeatures_1.10.1 gtable_0.1.2 Hmisc_3.10-1 labeling_0.1 [16] lattice_0.20-13 MASS_7.3-23 munsell_0.4 parallel_2.15.2 plyr_1.8 [21] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-3 Rsamtools_1.10.2 scales_0.2.3 [26] stats4_2.15.2 stringr_0.6.2 tools_2.15.2 XML_3.95-0.1 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org. ADD COMMENTlink modified 5.7 years ago by florian.hahne@novartis.com1.6k • written 5.8 years ago by Guest User12k 0 5.7 years ago by Switzerland Hi Joseph, Regarding your first problem: UCSC has no cytoband information for any of the zebrafish genomes, and that's what is throwing the error. I think it should do something smarter, e.g. use the chromosome length information that should be available for every UCSC genome to draw at least a blank ideogram which could still be used to indicate the current plotting position. I'll have this ready in the next release of the package, and maybe even port this back to the current release. It seems to be more of a bug than a missing feature? Your second problem is a bit more tricky. There is no real mapping between the ensembl genome names used in the Biomart package and the UCSC ones which I decided to take as the defaults for the package. I tried to come up with my own static mapping for this, and obviously this means that things tend to get out of date soon. Now the zebrafish version that you will get in Ensembl is Zv9 (which is equivalent to danRer7), but my mapping is still to danRer6. This is even wrong, because what you will get from Biomart if you ask for danRer6 now is actually danRer7. Yikes. I will have to come up with a better solution for this. There should be a way to explicitly control for the Ensembl genome that you will get, and this is a simple change. Getting it right automagically is way more challenging, I am afraid. As a quick fix for you: Ask for the danRer6 genes and manually change the genome of the track: biomTrack<-BiomartGeneRegionTrack(genome="danRer6",chromosome=1,start= 1e6,e nd=1e6+10000,name="ENSEMBL",showId=T) genome(biomTrack) <- "danRer7" I'll get back to you once I have a better solution. Florian -- On 1/16/13 9:10 PM, "Joseph Siefert [guest]" <guest at="" bioconductor.org=""> wrote: > >The first problem I have was with ideoTrack. I am using genome<-'danRer7' >and when I perform: >> genome<-"danRer7" >> myGene<-getGenes(cuff_data,'cdk6') >> myChr<-unique(features(myGene)$seqnames) >> ideoTrack <- IdeogramTrack(genome = genome, chromosome = myChr) > >I receive the following error message: > >Error in normArgTrack(track, trackids) : Unknown track: cytoBandIdeo > >I don't know how to get around this. I have tried to use chr1 for >chromosome and get same error. I have tried to use older versions of the >genome as well (i.e. 'danRer6', 'danRer5', etc. and receive the same >error). I have tried to use 'Zv9" and I get the error that it is not a >valid UCSC genome. I can use the human genome 'hg19' and for some >reason I don't understand it actually will pull up the zebrafish 'Zv9' >location, but this causes problems downstream with the biomaRt commands. > > >Secondly, I am having problems with the biomaRt command. When I enter >the command: >>biomTrack<-BiomartGeneRegionTrack(genome=genome,chromosome=as.charac ter(m >>yChr),start=myStart,end=myEnd,name="ENSEMBL",showId=T) > >I receive the following error: >Error in .genome2Dataset(genome) : >Unable to automatically determine Biomart data set for UCSC genome >'danRer7' > >The danRer7 is, but it will not automatically fetch the Biomart data set. > I have also tried using earlier versions of the zebrafish genome (i.e. >danRer6, danRer5, etc.) but I get the same error. Again, I have tried >using other names for the genome that may work for the biomaRt, such as >'Zv9' and 'Danio rerio genes (Zv9)', but then it tells me that it is not >a valid UCSC genome. Can you help me with this? > >Any and all help would be very much appreciated. Thanks so much > > -- output of sessionInfo(): > >R version 2.15.2 (2012-10-26) >Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > >locale: >[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >attached base packages: >[1] grid stats graphics grDevices utils datasets methods >base > >other attached packages: > [1] cummeRbund_2.0.0 Gviz_1.2.1 rtracklayer_1.18.2 >GenomicRanges_1.10.6 IRanges_1.16.4 fastcluster_1.1.7 > [7] reshape2_1.2.2 ggplot2_0.9.3 RSQLite_0.11.2 >DBI_0.2-5 BiocGenerics_0.4.0 > >loaded via a namespace (and not attached): > [1] AnnotationDbi_1.20.3 Biobase_2.18.0 biomaRt_2.14.0 >Biostrings_2.26.2 biovizBase_1.6.2 > [6] bitops_1.0-4.2 BSgenome_1.26.1 cluster_1.14.3 >colorspace_1.2-0 dichromat_1.2-4 >[11] digest_0.6.0 GenomicFeatures_1.10.1 gtable_0.1.2 >Hmisc_3.10-1 labeling_0.1 >[16] lattice_0.20-13 MASS_7.3-23 munsell_0.4 >parallel_2.15.2 plyr_1.8 >[21] proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-3 >Rsamtools_1.10.2 scales_0.2.3 >[26] stats4_2.15.2 stringr_0.6.2 tools_2.15.2 >XML_3.95-0.1 zlibbioc_1.4.0 > >-- >Sent via the guest posting facility at bioconductor.org.
Hi Florian, We actually have a small database called seqnames.db that is dedicated to tracking these kinds of chromosome name conventions. You can see more by looking at the help page for supportedSeqnameStyles() (and it's friends). A quick way to see that is: library(Homo.sapiens) ?supportedSeqnameStyles If you call the supportedSeqnameStyles() method, you will see that we don't (yet) have an entry for zebrafish. If you were to give me one as a tab file, I could add it to the database and it would therefore exist for the future... The file I need is deliberately simple to make. It should look like the example below, with as many columns as you want there to be styles for, and each column separated by a tab. NCBI MSU6 1 1 2 2 3 3 4 4 etc. Marc On 01/21/2013 09:15 AM, Hahne, Florian wrote: > Hi Joseph, > > Regarding your first problem: UCSC has no cytoband information for any of > the zebrafish genomes, and that's what is throwing the error. I think it > should do something smarter, e.g. use the chromosome length information > that should be available for every UCSC genome to draw at least a blank > ideogram which could still be used to indicate the current plotting > position. I'll have this ready in the next release of the package, and > maybe even port this back to the current release. It seems to be more of a > bug than a missing feature? > > Your second problem is a bit more tricky. There is no real mapping between > the ensembl genome names used in the Biomart package and the UCSC ones > which I decided to take as the defaults for the package. I tried to come > up with my own static mapping for this, and obviously this means that > things tend to get out of date soon. Now the zebrafish version that you > will get in Ensembl is Zv9 (which is equivalent to danRer7), but my > mapping is still to danRer6. This is even wrong, because what you will get > from Biomart if you ask for danRer6 now is actually danRer7. Yikes. I will > have to come up with a better solution for this. There should be a way to > explicitly control for the Ensembl genome that you will get, and this is a > simple change. Getting it right automagically is way more challenging, I > am afraid. > > As a quick fix for you: > Ask for the danRer6 genes and manually change the genome of the track: > biomTrack<-BiomartGeneRegionTrack(genome="danRer6",chromosome=1,star t=1e6,e > nd=1e6+10000,name="ENSEMBL",showId=T) > genome(biomTrack)<- "danRer7" > > I'll get back to you once I have a better solution. > > Florian > >

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