setRepository {annotate} | R Documentation

## 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 <mtmorgan@fhcrc.org>

### 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)

[Package annotate version 1.65.1 Index]