[BioC] how to unlock a package environment
Hervé Pagès
hpages at fhcrc.org
Thu Oct 1 21:41:31 CEST 2009
Forgot to send my sessionInfo(), sorry:
> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-24 r49817)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.5 genefilter_1.25.9
[4] ath1121501.db_2.3.5 org.At.tair.db_2.3.5 RSQLite_0.7-2
[7] DBI_0.2-4 AnnotationDbi_1.7.17 Biobase_2.5.8
loaded via a namespace (and not attached):
[1] annotate_1.23.4 splines_2.10.0 survival_2.35-7 tools_2.10.0
[5] xtable_1.5-5
H.
Hervé Pagès wrote:
> 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
> package:
>
> library(genefilter)
> library(hgu95av2.db)
> library(ath1121501.db)
> > genefilter:::.findCentralID("hgu95av2")
> [1] "ENTREZID"
> > genefilter:::.findCentralID("ath1121501")
> [1] "ACCNUM"
>
> Cheers,
> H.
>
>
> 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