[BioC] Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands

[Joseph Siefert [guest]]

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.character(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        

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