\HeaderA{neighborGeneFinder}{A widget for locating genes neighboring a target gene}{neighborGeneFinder}
\keyword{interface}{neighborGeneFinder}
\begin{Description}\relax
Given a set of data (matrix) with entries for LocusLink or UniGene
ids, the neighboring genes of a gene selected from a list on the
interface can be located.
\end{Description}
\begin{Usage}
\begin{verbatim}
neighborGeneFinder(geneData, keyName = c("unigene", "locuslink"),
organism = c("human", "mouse", "rat")) 
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{geneData}] \code{geneData} a matrix with columns named. The name
for one of the columns has to be either "locuslink" or "unigene"
\item[\code{keyName}] \code{keyName} a character string for the name of the
key columns of \code{geneData}. Has to be either "locuslink" or
"unigene"
\item[\code{organism}] \code{organism} a character string for the name of the
organism of interest. Has to be "human", "mouse", or "rat"
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Bioconductor's data package XXXCHRLLOC has to be instatlled for the
widget to work. If \code{keyName} is "unigene", XXXLLMappings is
required, where XXX is the name of the organism of interest.
\end{Details}
\begin{Value}
This function returns a list of lists. Elements of the top level list
are either LocusLink or UniGene ids. A sublist is inturn a list of
lists whose top level elements are chromosome numbers, each of which
is a list with an "upstream" and "downstream" elements.
\end{Value}
\begin{Note}\relax
This function is part of the Bioconductor project at Dana-Farber
Cancer Institute to provide Bioinformatics functionalities through R
\end{Note}
\begin{Author}\relax
Jianhua Zhang
\end{Author}
\begin{Examples}
\begin{ExampleCode}
  if(interactive()){
     require("annotate", character.only = TRUE) ||
     stop("Package annotate is not availble")
     geneData <- cbind(paste("100", 1:16, "_at", sep = ""), c(1, 50,
                       10044, 51, 71, 51371, 81, 51426, 188, 293, 360,
                       364, 375, 387, 513, 10572))
     colnames(geneData) <- c("Probe", "locuslink")
     neighborGeneFinder(geneData, "locuslink", "human")
  }
  
\end{ExampleCode}
\end{Examples}

