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

[Marc Carlson]

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 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 things tend to get out of date soon.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
>
>