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

[Hahne, Florian]

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 featureŠ

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things tend to get out of date soon.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.character(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.