[BioC] Category: testing for non-random chromosomal distribution of DE genes

[Marc Carlson]

Hi Paolo,

We already provide basic chromosome band information for flies. 
Therefore, it should be completely possible to just make adjustments to
the Category package to make this work.  However, the tricky part is
that human, mouse and fly all record such data is a slightly different
style of notation.  And so for supported organisms some extra
functionality would have to be added to Category in order to deal with
this.  If you are interested you might want to have a look at MAPcode.R
in the Category package.  There should already be examples there for
human and mouse.  If you have the time and inclination to make this
work, I would love to include your efforts so that everyone else can
benefit.


  Marc





Paolo Innocenti wrote:
> Hi all,
>
> I wanted to test for chromosomal region enriched for my list of DE genes.
> I tried with the ChrMapHyperGParams but it looks like that just Human
> and mice are supported (see below).
>
> I am really interested in this approach, and would like to know if it
> would be difficult to implement such support or there is any other
> package out there doing a similar job.
>
> If there is not a 'off the shelf' solution to this, the simplest
> possible question would be if my D.E. genes are enriched in sexual
> chromosomes vs. autosomes. Is there a better approach than a chisq.test?
>
> Thanks,
> paolo
>
> > temp.params <- new("ChrMapHyperGParams",
> +                  conditional=FALSE,
> +                  testDirection="over",
> +                  universeGeneIds=univ,
> +                  geneIds=id.int,
> +                  annotation=annotation(eset),
> +                  pvalueCutoff=0.05)
> > temp <- hyperGTest(temp.params)
> Error: 'ORGANISM:Drosophila melanogaster' is not a supported.
>  organism must be one of: ORGANISM:Homo sapiens, ORGANISM:Mus musculus
> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
>  [1] GOstats_2.10.0        graph_1.22.2          Category_2.10.0
>  [4] drosophila2.db_2.2.11 annaffy_1.16.0        affycoretools_1.16.0
>  [7] KEGG.db_2.2.11        GO.db_2.2.11          AnnotationDbi_1.6.0
> [10] affy_1.22.0           Biobase_2.4.1         RSQLite_0.7-1
> [13] DBI_0.2-4
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.12.0        annotate_1.22.0      biomaRt_2.0.0
>  [4] gcrma_2.16.0         genefilter_1.24.0    grid_2.9.0
>  [7] GSEABase_1.6.0       lattice_0.17-22      limma_2.18.0
> [10] lme4_0.999375-28     Matrix_0.999375-26   MCMCglmm_1.09
> [13] preprocessCore_1.6.0 RBGL_1.20.0          RCurl_0.94-1
> [16] splines_2.9.0        survival_2.35-4      tools_2.9.0
> [19] XML_2.3-0            xtable_1.5-5
>