setRepository: Functions to add arbitrary repositories
In annotate: Annotation for microarrays

Description Usage Arguments Details Author(s) Examples

These functions allow end users to add arbitrary repositories for use with the htmlpage function.

1
2
3

setRepository(repository, FUN, ..., verbose=TRUE)
getRepositories()
clearRepository(repository, verbose=TRUE)

`repository`	A character name for the repository.
`FUN`	A function to build hyperlinks for the repository. See details for more information.
`...`	Allows one to pass arbitrary code to underlying functions.
`verbose`	Output warning messages?

These functions allow end users to add, view, and remove repositories for use with the htmlpage function. getRepositories will output a vector of names for available repositories. clearRepository can be used to remove a repository if so desired. setRepository can be used to add a repository. See the examples section for the format of the FUN argument.

Once a new repository has been set, the htmlpage function can be called using the name of the new repository as a value in the repository argument (e.g., htmlpage(<other args>, repository = list("newrepositoryname"))

Martin Morgan <mtmorgan@fhcrc.org>

## A simple fake URI
repofun <- function(ids, ...)
paste("http://www.afakeuri.com/", ids, sep = "")

setRepository("simple", repofun)

## More complicated, we want to make sure that
## NAs get converted to empty cells

repofun <- function(ids, ...){
bIDs <- which(is.na(ids))
out <- paste("http://www.afakeuri.com/", ids, sep = "")
out[bIDs] <- "&nbsp;"
out
}

setRepository("complex", repofun)

## More complicated URI where we need to pass more information
## An example is Ensembl, which requires a species as part of the URI
## Since htmlpage() has an '...' argument, we can pass arbitrary
## arguments to this function that will be passed down to our
## repfun. Here we assume the argument species="Homo_sapiens" has been
## included in the call to htmlpage().


repofun <- function(ids, ...){
if(!is.null(list(...)$species))
      species <- list(...)$species
  else
      stop("To make links for Ensembl, you need to pass a 'species' argument.",
           call. = FALSE)
out <- paste("http://www.ensembl.org/", species, "/Search/Summary?species=",
              species, ";idx=;q=", ids, sep = "")
out
}

setRepository("species_arg", repofun)