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A RFC for dealing with annotation data.
Please comment on the following proposal.
In order to deal with the ever changing needs and continual evolution
of genomic data the annotate package must be able to update and
install annotation data.
It seems that this process is not unlike the R package system and
perhaps much can be gained by using features from both the package
system and the data system.
Functionality:
annotation: A function, like data, if given no argument it lists the
annotation that is available. Annotation is loaded using "data",
however.
There is an argument, local, if TRUE look on the local machine, if
FALSE, list available annotation datasets from Bioconductor.
We will use a different index file, 00Annotate.dcf in the annotate
data directory to hold this listing. It isn't really data and we
wouldn't really want people to get confused.
install.annotation: Takes a base name (like "hgu95A") and obtains and
installs a package from the bioconductor web site (using the same
system of URL access as install.packages).
This will download data, put it in the appropriate directory and
update the index file.
update.annotation: Takes a base name (like "hgu95A") and checks to see
if it needs to be updated.
I still need to figure out how to automagically build this stuff but
would like to get comments quickly so it can be squeezed in to the
release.
thanks
robert
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