[BioC] Arabidopsis chromosome location mappings

Marc Carlson mcarlson at fhcrc.org
Mon Oct 6 18:11:52 CEST 2008

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,


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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