[BioC] how to unlock a package environment

Hervé Pagès hpages at fhcrc.org
Thu Oct 1 21:38:30 CEST 2009

Hi Ariel,

One solution is that you use the development version of Bioconductor
(BioC 2.5, to be released soon, based on the R-2.10 series).

In the development version of genefilter it looks like the nsFilter()
function has been improved in order to deal properly with the
peculiarity of the ath1121501.db package. Internally it's now
calling a little helper function .findCentralID() (not exported)
in order to determine what's the central ID in the annotation

   > genefilter:::.findCentralID("hgu95av2")
   [1] "ENTREZID"
   > genefilter:::.findCentralID("ath1121501")
   [1] "ACCNUM"


Ariel Chernomoretz wrote:
> Hi all,
> I am currently analyzing some arabidopsis thaliana experiments (ath1121501
> GeneChip)
> The corresponding annotation package, ath1121501.db, is a little bit
> 'special' as
> there is no ENTREZID map for the chip.
> I would like to cheat and create  a fake ath1121501ENTREZID for the
> environment as a copied instance of ath1121501ACCNUM (in order to use, for
> instance,  the genefilter package's function "nsFilter" to deal with non
> annotated, or duplicated probesets)
> The problem is that I am not able to create a new entry in the
> package:ath112150.db as it is a locked environment. Is there any way to
> temporarily unlock it, do some stuff and lock it again?
> (It seems easy to lock environments, using the lockEnvironment function, but
> I did not find an easy way to unlock them)
> Thanks in advance
> Ariel./

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

More information about the Bioconductor mailing list