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_N
AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI
FICATION=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
--
Paolo Innocenti
Department of Animal Ecology, EBC
Uppsala University
Norbyv?gen 18D
75236 Uppsala, Sweden
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_IDEN
TIFICATION=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
>