\Header{getSYMBOL}{Functions to deal with Data Packages}
\alias{contents}{getSYMBOL}
\alias{getGO}{getSYMBOL}
\alias{getGOdesc}{getSYMBOL}
\alias{getLL}{getSYMBOL}
\alias{getPMID}{getSYMBOL}
\keyword{manip}{getSYMBOL}
\begin{Description}\relax
The functions documented here are intended to make it easier to map
from a set of manufacturers identifiers (such as you will get from the
chips etc) to other identifiers.\end{Description}
\begin{Usage}
\begin{verbatim}
getSYMBOL(x, data)
getLL(x, data)
getGO(x, data)
getPMID(x, data)
getGOdesc(x, which=c("MF","BP","CC") )
contents(object)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] The identifiers to be mapped (usually manufacturer)
\item[\code{data}] A character string identifying the data source 
\item[\code{which}] For \code{getGOdesc} indicates which GO hierarchy to use.
\item[\code{object}] The environment (data table) that you want to get all
contents from
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Appropriate translations are done. In some cases such as \code{getLL}
and \code{getSYMBOL} there will only be one match and a vector is
returned. In other cases such as \code{getPMID} and \code{getGO} there
may be multiple matches and a list is returned.
For \code{getGOdesc} the input vector is GO identifiers (not
manufacturer identifiers) and in the output any identifier that does
not have a description in the selected GO hierarchy (MF, BP or CC) is
dropped.\end{Details}
\begin{Value}
Either a vector or a list depending on whether multiple values per
input are possible.\end{Value}
\begin{Author}\relax
R. Gentleman\end{Author}
\begin{SeeAlso}\relax
\code{\Link{multiget}}\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  data(eset)
  gN <- geneNames(eset)[100:105]
   ## A bit of a hack to not have a package dependency on hgu95av2
   ## but need to fiddle w/ the warn level to not fail the example anyways.
   curWarn <- getOption("warn")
   options(warn=0)
   on.exit(options(warn=curWarn), add=TRUE)
  if( require("hgu95av2", character.only=TRUE)
       && require("GO", character.only=TRUE) ) {
      getSYMBOL(gN,"hgu95av2" )
      gg<- getGO(gN, "hgu95av2")
      getGOdesc(gg[[2]], "MF")
      getLL(gN, "hgu95av2")
      getPMID(gN, "hgu95av2")
  } else
   cat("could not run all examples\n")
\end{ExampleCode}
\end{Examples}

