[BioC] Using annotation maps as environments in packages
Antti Honkela
antti.honkela at tkk.fi
Thu Mar 4 19:18:25 CET 2010
Hi all,
I have a weird problem when I try to write a function in a package
that would use annotation maps (e.g. mouse430a2SYMBOL) as an
environment that the function works on its own breaks when moved into
a package.
The maps can usually be used as environments without problems and the
following works fine:
> library(mouse430a2.db)
> get("1419728_at", env=mouse430a2SYMBOL)
The same is true if I define an own function to access the map, and
this runs without problems:
> getAnnotation <- function(gene, env) { return (get(gene, env=env)) }
> getAnnotation("1419728_at", env=mouse430a2SYMBOL)
However, if I move the same function definition to an independent
package, the same call results in an error:
> getAnnotation("1419728_at", env=mouse430a2SYMBOL)
Error in get(gene, env = env) : invalid 'envir' argument
Any ideas how to fix or circumvent this?
(Note that in the sessionInfo below, testpkg is a minimal package only
containing the above function definition.)
Best regards,
Antti
---------------------------------------------------------
> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] mouse430a2.db_2.3.5 org.Mm.eg.db_2.3.6 RSQLite_0.7-3
DBI_0.2-4 AnnotationDbi_1.8.1 Biobase_2.6.0
[7] testpkg_0.0-1
loaded via a namespace (and not attached):
[1] affy_1.24.2 affyio_1.14.0 preprocessCore_1.8.0
--
Antti Honkela
Antti.Honkela at tkk.fi - http://www.cis.hut.fi/ahonkela/
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