setRepository: Functions to add arbitrary repositories

In Bioconductor/annotate: Annotation for microarrays

Functions to add arbitrary repositories

Description

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

Usage

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

Arguments

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?

Details

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"))

Author(s)

Martin Morgan <[e-mail]>

Examples

## 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)

Bioconductor/annotate documentation built on Nov. 2, 2024, 4:40 p.m.