Thanks a lot, Marc,

I do not know of a reliable source for the chromosome lengths information.

So I guess that would make it impossible to make chromosome plots for
Arabidopsis data.... I ll try to somehow get around that,

best wishes and thanks again.

Samuel

2008/10/6 Marc Carlson <mcarlson@fhcrc.org>

> Hi Samuel,
>
> The CHRLENGTHS mapping would just be a vector of all named chromosome
> lengths for Arabidopsis.  If we had one for arabidopsis, it would not
> contain the the chromosome locations mappings for much of anything.  We
> normally get CHRLENGTHS mapping information from UCSC, but unfortunately
> they don't cover Arabidosis there, so we don't have a source for this
> information.  But since all this is, is a named vector of the chromosome
> lengths, then if you know this information, you could probably fill it
> in pretty easily by just creating a named vector.  Also, if you have a
> recommendation for a reliable public source of this information that is
> considered trustworthy by the arabidopsis community for this, please
> tell me about it so that we can know about it too.
>
> If you really want the location of the start of these genes along the
> chromosomes, that information (from TAIR) is present in the
> ath1121501CHRLOC mapping.  And if you want the ends, then you can find
> those in the ath1121501CHRLOCEND mapping (but this last mapping is only
> found in the most recent devel packages).
>
> Please let me know if I answered your questions,
>
>
>  Marc
>
>
>
>
> Samuel Wuest wrote:
> > Hi,
> >
> > Hope you're fine…
> > I am trying to make whole genome plots using the geneplotter
> > package/annotate package. The organism I am studying is Arabidopsis
> > thaliana, and obviously the annotations are not so extensive there: when
> > trying to build a chromLocation object, I can't obviously do that (see
> error
> > below)
> > It is obvious to me, that the chromosome location mappings are not
> provided
> > in the Arabidopsis anntation package (see below).
> >
> > My question: is there any way of plotting Arabidopsis gene expression
> data
> > along a chromosome. Should I just order the GeneIds (luckily, for the
> TAIR
> > Ids one can infer the gene order along a chromosome)? Has anyone made a
> > script for this?
> >
> > Thanks for any help, best wishes,
> >
> > Sam
> >
> >
> >
> >> library(ath1121501.db)
> >> newChrClass <- buildChromLocation("ath1121501")
> >>
> > Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
> >   variable "ath1121501CHRLENGTHS" was not found
> >
> >
> >> objects("package:ath1121501.db")
> >>
> >  [1] "ath1121501"             "ath1121501ACCNUM"
> > "ath1121501ARACYC"       "ath1121501ARACYCENZYME" "ath1121501CHR"
> >  [6] "ath1121501CHRLOC"       "ath1121501ENZYME"
> > "ath1121501ENZYME2PROBE" "ath1121501GENENAME"     "ath1121501GO"
> > [11] "ath1121501GO2ALLPROBES" "ath1121501GO2PROBE"
> > "ath1121501MAPCOUNTS"    "ath1121501MULTIHIT"     "ath1121501ORGANISM"
> > [16] "ath1121501PATH"         "ath1121501PATH2PROBE"
> > "ath1121501PMID"         "ath1121501PMID2PROBE"   "ath1121501SYMBOL"
> > [21] "ath1121501_dbInfo"      "ath1121501_dbconn"
> > "ath1121501_dbfile"      "ath1121501_dbschema"
> >
> >
> >> sessionInfo()
> >>
> > R version 2.7.0 (2008-04-22)
> > i386-apple-darwin8.10.1
> >
> > locale:
> > en_IE.UTF-8/en_IE.UTF-8/C/C/en_IE.UTF-8/en_IE.UTF-8
> >
> > attached base packages:
> > [1] tools     stats     graphics  grDevices utils     datasets  methods
> > base
> >
> > other attached packages:
> >  [1] ath1121501.db_2.2.0  TinesATH1.db_1.0     geneplotter_1.18.0
> > annotate_1.18.0      xtable_1.5-2         AnnotationDbi_1.2.0
> >
> >       [[alternative HTML version deleted]]
> >
> >
> > ------------------------------------------------------------------------
> >
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